# restart R session
#.rs.restartR()
rm(list=ls())

system("hostname")
print(Sys.Date())
## [1] "2021-11-29"
print(Sys.time())
## [1] "2021-11-29 20:21:40 EST"
libs <- c("limma", "minfi", "ggpubr", "DMRcate", "gProfileR", "gplots", "QQperm", "DOSE", "enrichplot", "clusterProfiler", "org.Hs.eg.db", "R.utils", "knitr", "gprofiler2","ggpubr","gridExtra", "grid", "ggplot2", "lattice", "ggnewscale", "magrittr", "msigdbr")

for (l in libs) {
  if (require(l, character.only = T)) {
    print(paste0(l, " loaded successfully"))
  } else {
    install.packages(l)
    require(l, character.only = T)
    print(paste0(l, " installed and loaded successfully"))
  }
}
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## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## 
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## Loading required package: locfit
## locfit 1.5-9.4    2020-03-24
## Setting options('download.file.method.GEOquery'='auto')
## Setting options('GEOquery.inmemory.gpl'=FALSE)
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## Loading required package: ggpubr
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## Warning: replacing previous import 'minfi::getMeth' by 'bsseq::getMeth' when
## loading 'DMRcate'
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## 
## DOSE v3.16.0  For help: https://guangchuangyu.github.io/software/DOSE
## 
## If you use DOSE in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609
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## Loading required package: clusterProfiler
## clusterProfiler v3.18.1  For help: https://guangchuangyu.github.io/software/clusterProfiler
## 
## If you use clusterProfiler in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
## 
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# Save result files with timeStamp
timeStamp <- as.character(round(unclass(Sys.time())))
print(timeStamp)
## [1] "1638235354"
sig_digits <- 2
sum_sd <- function(data, varname) {
    eval(parse(text = str_c("data[, round(summary(", varname, "), digits=2)] %>% print()")))
    eval(parse(text = str_c("print(str_c('SD: ', data[, sd(", varname, ", na.rm = T) %>% 
                                round(sig_digits)]))")))
}

1. Data locations and loading

fhs.dir="/udd/reprk/projects/TOPMed/DNAm_data"
res.dir = "/proj/regeps/regep00/studies/CAMP/analyses/reprk/methylation/results/IgE_paper"
sub.plots.dir = file.path(res.dir, "plots")

merge_CG <- read.table(file=file.path(res.dir,
                  "CAMP_CRA_DMPs_fdr_logIgE_hg19_overlap_1630601015.txt"),
                  header=T,stringsAsFactors=F,sep='\t', quote="")
dim(merge_CG)
## [1] 10426    62
load(file=file.path(res.dir, "../norm.betas.camp_rcp_hg19_clean_allchr_1620830489.RData"))
norm.betas.rcp<-NULL;rm(norm.betas.rcp)
dim(ann850k)
## [1] 865859     46
merge_CG.all <- read.table(file=file.path(res.dir,
                  "CAMP_CRA_FHS_DMPs_fdr_logIgE_hg19_overlap_1630601015.txt"),
                  header=T,stringsAsFactors=F,sep='\t', quote="")
dim(merge_CG.all)
## [1] 193  92
# don't need to load FHS results for this, just the overlapping sites between all datasets as above
#fhs.fdr <- read.csv(file=file.path(fhs.dir, 
#                    "IgE_offGen3_sample3471_adjSVp01_cellnoEOS_fdr5.csv"),
#                    as.is=TRUE, sep = ",", stringsAsFactors=FALSE)

2. Data prep for enrichment analysis

# one of the issues could be that FHS is 450K and CRA/CAMP is 850K so for now I am using the 850K gene list of the platform as background. Ideally, I would have taken the overlap of genes annotated to the CpGs tested in all datasets under analysis as the background, but with different platforms, not sure about the best approach here

ann850k$Gene <- sub(";.*", "", ann850k$UCSC_RefGene_Name);
uniq.ge.plt <- unique(ann850k$Gene)

uniq.ge.plt <- uniq.ge.plt[uniq.ge.plt!="NA"]
uniq.ge.plt <- uniq.ge.plt[uniq.ge.plt!=""]
length(uniq.ge.plt)
## [1] 26644
head(uniq.ge.plt)
## [1] "DDX11L1"      "WASH5P"       "OR4F5"        "LOC101928626" "MIR1977"     
## [6] "LOC100133331"
write.table(uniq.ge.plt, file=file.path(res.dir, 
            paste0("uniq_background_genes_platform_", timeStamp, ".txt")), 
            sep="\t", quote=F, row.names=F)

uniq.hyper <- merge_CG[merge_CG$Direction_camp_cra=="++",]
uniq.hyper <- unique(uniq.hyper$Gene.x)
uniq.hyper <- uniq.hyper[uniq.hyper!="NA"]
uniq.hyper <- uniq.hyper[uniq.hyper!=""]
length(uniq.hyper)
## [1] 1025
write.table(uniq.hyper, file=file.path(res.dir, 
              paste0("cra_camp_uniq_hypermeth_genes_", timeStamp, ".txt")),
            sep="\t", quote=F, row.names=F)

uniq.hypo <- merge_CG[merge_CG$Direction_camp_cra=="--",]
uniq.hypo <- unique(uniq.hypo$Gene.x)
uniq.hypo <- uniq.hypo[uniq.hypo!="NA"]
uniq.hypo <- uniq.hypo[uniq.hypo!=""]
length(uniq.hypo)
## [1] 3520
write.table(uniq.hypo, file=file.path(res.dir, 
              paste0("cra_camp_uniq_hypometh_genes_", timeStamp, ".txt")), 
              sep="\t", quote=F, row.names=F)

3. enrichment gprofiler2 for CRA and CAMP

enrich.hyper <- gprofiler2::gost(query=uniq.hyper, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))
## Detected custom background input, domain scope is set to 'custom'
names(enrich.hyper)
## [1] "result" "meta"
# Results containing all annotated terms for hyper-methylated CpGs
gem <- enrich.hyper$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)
##             GO.ID        Description term_size intersection_size Domain
## 1497 MIRNA:000000         MIRNA root     14165               749  MIRNA
## 747    GO:0003674 molecular_function     17356               844  GO:MF
## 748    GO:0005515    protein binding     13924               726  GO:MF
## 749    GO:0005488            binding     15946               794  GO:MF
## 586    GO:0005737          cytoplasm     11268               618  GO:CC
## 587    GO:0005575 cellular_component     17335               831  GO:CC
##               FDR Phenotype
## 1497 9.523048e-32        +1
## 747  4.230697e-29        +1
## 748  1.889285e-26        +1
## 749  2.472457e-26        +1
## 586  1.431912e-23        +1
## 587  1.431912e-23        +1
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Genes
## 1497                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ZMIZ1,TGFBR2,C20orf27,GSG1,KIF5C,TREM2,XYLT1,ABL1,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,UCK2,VAV2,DAAM1,KIF13B,MPO,ASB1,PCGF3,LPP,MGAT5,CAMKK2,KIAA1549L,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,LYPD4,CHST11,TERF2,PREX1,MDC1,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,PRKCH,PSMB7,GM2A,INTS6,SSH2,VPS13B,FAM193B,ZDHHC14,CD244,SH3PXD2B,PPM1H,RNF44,SLC36A1,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,TNS1,TTC7B,IFFO2,KLHL25,GAS7,GALNT14,CDCP1,CLEC5A,GLIPR2,OPRM1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,CAMK1D,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,KIAA0586,DYM,TNF,RPTOR,CCDC149,PECR,FKBP5,MTAP,AFF4,LARP1,BAZ1B,LIPA,UBN1,PML,NSMCE2,PXYLP1,ASAP2,B4GALNT3,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,TMC7,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,FAM168A,SFXN5,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,PIK3C2B,EPHB3,PROSER2,VTI1A,DLEU1,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,HRH1,KIAA0513,ETV6,SEPT9,PRPF6,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,NAV3,TFDP1,NCKAP5L,NR3C1,VIT,PXN,SDCCAG8,AP1G1,MYOF,NID1,POR,SESTD1,SULT1B1,MAML2,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,FAM227B,DISC1,GAPVD1,MORC3,PEMT,CCDC102A,LAPTM4A,TAOK3,RIN2,SYNPO,GALNT2,MYH9,RGL1,PLEKHM3,KDM5B,AKAP13,LMTK2,OXR1,RFX3,LINGO1,CD300LG,BCL11A,GPR55,XXYLT1,SLC24A4,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,TACC3,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,MCF2L2,SLC25A18,ART5,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,ITGA5,AKAP2,C20orf144,B4GALT5,STOX2,TNFRSF11A,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,ATP2B4,SLC38A1,UST,NFYC,S100A12,BLM,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,AGRP,FAM53B,ZNF827,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,ZCCHC24,PIGR,INPP5D,IL6R,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,SURF6,RERE,VNN2,ERAP1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,TNFRSF9,KIAA0825,SAMD4A,S100A9,FAM13A,AP1B1,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,TMEM105,SNX10,UBAC2,SLC39A10,HS3ST3B1,DNAL4,HMGCL,CTSD,TREM1,PRMT5,TMEM63A,IL27,TBXAS1,IL1R1,ADARB1,NAV2,GPLD1,ERGIC1,UXS1,LY6H,SDC2,SLC45A4,PRR5L,STK24,TMEM182,SYN3,SUSD6,CSF1,TRAF1,RAD54L2,PLCB1,RAD9B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,S100A8,PRDM2,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,ZNF516,ECM2,PI4K2A,LPIN2,KIAA0195,HSPG2,AP3S2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,GOLIM4,NLN,TMCO3,RAP1GAP2,MBOAT2,TMEM72,SWAP70,TIAM1,PANX1,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,PIM3,DUSP16,RASA3,PRKCD,ZSWIM7,FOXN3,DSTYK,POU2F3,ABCD4,CECR2,AADACL3,SBNO2,ZBTB47,RNF40,HSPA4L,NQO2,MGLL,NANOG,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,ARID3B,TOM1L2,CCDC69,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,CPAMD8,PAG1,GAS8,FEZ2,WDFY3,ENO1,SPRED2,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,SDHAF3,ZNF319,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,GXYLT2,SULF2,MYO5A,ZMYND11,C16orf70,FAM126A,CCDC30,ADRA1A,TSPAN18,GTDC1,FNDC3B,CALML4,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,MAST3,CDC42BPB,DNMT3A,CTSH,TSPAN3,PPM1M,PRPSAP1,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,SLC37A2,NDUFA10,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,DOT1L,KCNJ15,GPATCH2,RGS3,AVPI1,LMF1,TM9SF4,RBM33,SLCO2A1,KIAA1549,RAB31,ADK,SETD1A,CPNE6,MPRIP,WDHD1,CCDC34,ADPGK,TNIP3,SMAD1,GPRIN3,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,SLC6A6,DGKI,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,POLA2,SV2C,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,DIP2C,ABCC2,MBP,CACHD1,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ERI3,GABBR1,APBB1,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,FSTL4,ZDHHC24,NCLN,LRIG1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1
## 747  TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,CHST11,TERF2,PREX1,SLC36A3,PRKAG2,MDC1,ABCA9,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,GM2A,INTS6,SSH2,MOK,FAM193B,ZDHHC14,CD244,SH3PXD2B,PPM1H,LRRK1,RNF44,SLC36A1,CTSG,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,KLHL25,GAS7,GALNT14,CDCP1,ACOXL,CLEC5A,GLIPR2,DLEU7,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,PTX4,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,LIPA,UBN1,PML,NSMCE2,PXYLP1,ASAP2,B4GALNT3,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,TMC7,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,FAM168A,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,RGL4,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,PROSER2,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,HRH1,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,VIT,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,GPR68,NID1,POR,SESTD1,SULT1B1,MAML2,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,CCDC102A,LAPTM4A,TAOK3,RIN2,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,GPR55,XXYLT1,SLC24A4,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,SH3RF3,ITGAE,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,MCF2L2,PDZK1IP1,SLC25A18,ART5,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,B4GALT5,STOX2,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,CCDC148,ATP2B4,SLC38A1,UST,CYP3A7-CYP3A51P,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,ZCCHC24,PIGR,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,KIAA0825,SAMD4A,S100A9,FAM13A,AP1B1,PHF11,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,SLC39A10,HS3ST3B1,DNAL4,HMGCL,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,IL1R1,ADARB1,GIMAP1-GIMAP5,HHIPL2,NAV2,GPLD1,ERGIC1,UXS1,LY6H,SDC2,SLC45A4,PRR5L,STK24,TMEM182,SEMA4A,SYN3,SUSD6,CSF1,TRAF1,TSGA13,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,IDO2,S100A8,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,ZNF516,ECM2,PI4K2A,LPIN2,HSPG2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,NLN,TMCO3,RAPSN,RAP1GAP2,MBOAT2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,ZSWIM7,FOXN3,DSTYK,POU2F3,ABCD4,CECR2,AADACL3,SBNO2,ZBTB47,RNF40,RNASE11,HSPA4L,NQO2,CSF3,MGLL,GLIS1,NANOG,AK5,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,DRGX,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,RNASE9,ZNF319,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,GXYLT2,SULF2,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,GTDC1,FNDC3B,CALML4,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,CATIP,MAST3,CDC42BPB,DNMT3A,CTSH,TSPAN3,PPM1M,ZNF385C,PRPSAP1,OTUD6B,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,SLC37A2,ARMC9,NDUFA10,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,FHAD1,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,GLT1D1,AVPI1,TM9SF4,HLA-DMB,RBM33,SLCO2A1,RAB31,ADK,SETD1A,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,CCDC34,ADPGK,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,SLC6A6,DGKI,WDR49,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,DIP2C,ABCC2,MBP,ELOVL3,CACHD1,RNF216,USP47,PPP1R13B,ANO10,SCYL2,AP3M2,ERI3,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,BPIFB1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## 748                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,COL23A1,LRRC27,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,CAMKK2,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,TERF2,PREX1,PRKAG2,MDC1,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,INTS6,SSH2,FAM193B,CD244,SH3PXD2B,PPM1H,LRRK1,RNF44,SLC36A1,CTSG,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,TNS1,TTC7B,KLHL25,GAS7,CDCP1,GLIPR2,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,NISCH,SFMBT2,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,SPARC,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,UBN1,PML,NSMCE2,PXYLP1,ASAP2,SMG6,OTUB2,TPD52L2,ROPN1L,PCNT,RALGAPA2,IRAK2,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,FAM168A,SFXN5,FCN1,AFAP1,SLC25A37,KCTD10,LRP3,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,PROSER2,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,KIF21B,PCSK6,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,NID1,POR,SESTD1,SULT1B1,WDR20,RAB11FIP1,FNDC3A,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,LAPTM4A,TAOK3,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,EPHA2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,SH3RF3,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,PDZK1IP1,SLC25A18,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,CCDC148,ATP2B4,SLC38A1,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,KIAA0825,SAMD4A,S100A9,AP1B1,PHF11,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,DNAL4,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,IL1R1,ADARB1,HHIPL2,NAV2,ERGIC1,UXS1,LY6H,SDC2,PRR5L,STK24,TMEM182,SEMA4A,SUSD6,CSF1,TRAF1,TSGA13,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,S100A8,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,ECM2,PI4K2A,HSPG2,HTR3A,ARFIP1,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,SCARF1,MIER2,RAPSN,RAP1GAP2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,MAPKAPK2,UBE2L6,PIM3,DUSP16,CHI3L1,PRKCD,ZSWIM7,FOXN3,POU2F3,ABCD4,CECR2,SBNO2,ZBTB47,RNF40,RNASE11,NQO2,CSF3,MGLL,GLIS1,NANOG,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,XRCC5,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,JDP2,CERS6,ACTN1,BACE1,MAP2K6,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,ZNF319,CYB561,SENP5,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,FNDC3B,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,CATIP,MAST3,CDC42BPB,DNMT3A,CTSH,ZNF385C,PRPSAP1,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,ARMC9,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,FHAD1,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,AVPI1,TM9SF4,HLA-DMB,SLCO2A1,RAB31,SETD1A,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,CCDC34,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,DGKI,WDR49,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,ABCC2,MBP,ELOVL3,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## 749                                                                                                                                                                                                                                                                                                                                         TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,TERF2,PREX1,PRKAG2,MDC1,ABCA9,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,INTS6,SSH2,MOK,FAM193B,CD244,SH3PXD2B,PPM1H,LRRK1,RNF44,SLC36A1,CTSG,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,KLHL25,GAS7,GALNT14,CDCP1,ACOXL,CLEC5A,GLIPR2,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,PTX4,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,UBN1,PML,NSMCE2,PXYLP1,ASAP2,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,FAM168A,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,PROSER2,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,VIT,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,NID1,POR,SESTD1,SULT1B1,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,LAPTM4A,TAOK3,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,XXYLT1,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,SH3RF3,ITGAE,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,PDZK1IP1,SLC25A18,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,B4GALT5,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,CCDC148,ATP2B4,SLC38A1,CYP3A7-CYP3A51P,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,ZCCHC24,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,KIAA0825,SAMD4A,S100A9,AP1B1,PHF11,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,DNAL4,HMGCL,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,IL1R1,ADARB1,GIMAP1-GIMAP5,HHIPL2,NAV2,ERGIC1,UXS1,LY6H,SDC2,PRR5L,STK24,TMEM182,SEMA4A,SYN3,SUSD6,CSF1,TRAF1,TSGA13,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,IDO2,S100A8,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,ZNF516,ECM2,PI4K2A,HSPG2,HIVEP3,HTR3A,ARFIP1,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,NLN,RAPSN,RAP1GAP2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,ZSWIM7,FOXN3,DSTYK,POU2F3,ABCD4,CECR2,SBNO2,ZBTB47,RNF40,RNASE11,HSPA4L,NQO2,CSF3,MGLL,GLIS1,NANOG,AK5,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,DRGX,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,RNASE9,ZNF319,CYB561,SENP5,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,SULF2,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,FNDC3B,CALML4,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,CATIP,MAST3,CDC42BPB,DNMT3A,CTSH,PPM1M,ZNF385C,PRPSAP1,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,ARMC9,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,FHAD1,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,AVPI1,TM9SF4,HLA-DMB,RBM33,SLCO2A1,RAB31,ADK,SETD1A,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,CCDC34,ADPGK,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,DGKI,WDR49,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,ABCC2,MBP,ELOVL3,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ERI3,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,BPIFB1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## 586                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           TFR2,ZMIZ1,TGFBR2,GSG1,RBKS,KIF5C,XYLT1,ABL1,RUFY4,CARS,ATN1,GALNT6,CELF2,COL23A1,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,LPP,MGAT5,CAMKK2,POC1B,DTNB,TPP1,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CAMK2G,PSMF1,NLRC4,CHST11,TERF2,PREX1,PRKAG2,NDUFS2,SORCS2,WDFY4,DENND2D,VDR,FIG4,TOR3A,TRIM67,LIPC,SSH1,FOXK1,ITPKC,WDFY1,IRF5,SVIL,PRKCH,PSMB7,GM2A,SSH2,MOK,FAM193B,ZDHHC14,SH3PXD2B,PPM1H,LRRK1,SLC36A1,CTSG,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,KLHL25,GAS7,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,NEDD9,ZFR,MKNK1,NISCH,SFMBT2,CAMK1D,NGF,RBSN,EPB41L3,ARG1,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,PPM1F,RHBDF2,CUX1,ARSG,SPARC,KIAA0586,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,MEFV,LARP1,LIPA,PML,PXYLP1,ASAP2,B4GALNT3,SMG6,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,MVP,PPP2R5C,EFR3B,DAGLB,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,MTMR7,ARRDC5,MARCO,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,RGL4,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,FKBP15,SYNJ2,STX8,ABCA13,ALDH2,CCRL2,NAE1,ITPR1,UBASH3B,TMEM150B,CRYL1,MIF4GD,LYN,TGOLN2,RETN,PIK3C2B,EPHB3,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,HIPK3,KIF21B,PCSK6,HRH1,KIAA0513,ETV6,SEPT9,MYCBPAP,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,UPB1,TFDP1,NCKAP5L,NR3C1,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,POR,SULT1B1,CCDC63,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,TSKS,PEMT,LAPTM4A,TAOK3,RIN2,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,OXR1,CD300LG,BCL11A,XXYLT1,SLC24A4,LARS2,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,RGCC,USP10,PRKCE,ZBTB20,CHST15,SLC25A18,SEMA4C,ASPH,HCN4,MERTK,SERPINA1,PSAP,SBF2,TMC8,ANTXR1,KRT17,B4GALT5,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,ATP2B4,UST,IGFBP6,S100A12,PSEN2,BLM,IL16,HIVEP1,HEBP2,DENND3,MYADM,FGD5,AGRP,SRGAP3,RAB40C,ECE1,SLAIN1,LHFPL2,TBC1D14,PIGR,INPP5D,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,SERTAD2,TRIO,TMC6,FAP,SAMD4A,S100A9,FAM13A,AP1B1,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,RGS14,CYTH3,RAB5C,NOL4L,TCF3,ITPKB,SNX10,UBAC2,HS3ST3B1,DNAL4,HMGCL,CTSD,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,ADARB1,GIMAP1-GIMAP5,GPLD1,ERGIC1,UXS1,SDC2,STK24,SYN3,CSF1,TRAF1,PLCB1,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,TRAK1,OTUB1,PASK,IDO2,S100A8,CFAP61,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,PI4K2A,LPIN2,HSPG2,AP3S2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,ARAP2,ANXA6,OGG1,MTF1,BECN1,IL18,UGCG,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,GOLIM4,NLN,RAPSN,RAP1GAP2,MBOAT2,SWAP70,TIAM1,PANX1,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,DSTYK,POU2F3,ABCD4,RNF40,HSPA4L,NQO2,MGLL,AK5,PDE4B,MYO1F,AATK,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,GSN,NOS1AP,GDPD5,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,TOM1L2,CCDC69,XRCC5,ABCA3,DOCK10,DPYSL3,CPEB4,RASAL2,LMO7,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,SDHAF3,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,GJB6,AJUBA,EIF4G1,SORL1,TJAP1,VAC14,SULF2,MYO5A,C16orf70,FAM126A,ADRA1A,DLC1,CCDC92,DENND1A,FCHSD2,HEYL,ST6GAL1,CATIP,CDC42BPB,DNMT3A,CTSH,PRPSAP1,OTUD6B,HAVCR2,IQCG,CTNNBIP1,PDGFD,SLC37A2,ARMC9,NDUFA10,STXBP2,ATP11B,BCAS4,CYSTM1,CCDC88C,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,FLYWCH1,MACF1,IL22RA2,RGS3,GLT1D1,LMF1,TM9SF4,HLA-DMB,RAB31,ADK,CPNE6,MPRIP,WDHD1,ADPGK,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,RNF144A,DGKI,SERPINB13,SIK3,EPHA4,CACNA1C,HRC,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,MBP,ELOVL3,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ICA1,GABBR1,PPP1R1B,APBB1,USP25,FAM83D,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,ANKS6,CXADR,TMEM30A,PPM1E,VAMP1,STARD9
## 587                                                                                  TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,KIAA1549L,CDCP2,POC1B,DTNB,FAM180B,TPP1,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,FBN2,CAMK2G,PSMF1,NLRC4,LYPD4,CHST11,TERF2,PREX1,SLC36A3,PRKAG2,MDC1,ABCA9,NDUFS2,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,GM2A,INTS6,SSH2,MOK,FAM193B,ZDHHC14,CD244,SH3PXD2B,PPM1H,LRRK1,SLC36A1,CTSG,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,IFFO2,KLHL25,GAS7,GALNT14,CDCP1,ACOXL,CLEC5A,GLIPR2,DLEU7,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,PTX4,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,KIAA0586,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,LIPA,UBN1,PML,NSMCE2,PXYLP1,ASAP2,B4GALNT3,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,TMC7,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,RGL4,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,NAE1,ITPR1,UBASH3B,BTN2A2,TMEM150B,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,HRH1,KIAA0513,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,VIT,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,GPR68,NID1,POR,SESTD1,SULT1B1,CCDC63,MAML2,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,CCDC102A,LAPTM4A,TAOK3,RIN2,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,GPR55,XXYLT1,SLC24A4,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,ITGAE,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,PDZK1IP1,SLC25A18,ART5,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,B4GALT5,STOX2,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,ATP2B4,SLC38A1,UST,CYP3A7-CYP3A51P,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,PIGR,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,SAMD4A,S100A9,FAM13A,AP1B1,PHF11,GFI1,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,SLC39A10,HS3ST3B1,DNAL4,HMGCL,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,IL1R1,ADARB1,GIMAP1-GIMAP5,HHIPL2,NAV2,GPLD1,ERGIC1,UXS1,LY6H,SDC2,SLC45A4,PRR5L,STK24,TMEM182,SEMA4A,SYN3,SUSD6,CSF1,TRAF1,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,IDO2,S100A8,CFAP61,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,ZNF516,ECM2,PI4K2A,LPIN2,KIAA0195,HSPG2,AP3S2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,GOLIM4,NLN,TMCO3,RAPSN,RAP1GAP2,MBOAT2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,ZSWIM7,FOXN3,DSTYK,OCSTAMP,POU2F3,ABCD4,CECR2,AADACL3,SBNO2,ZBTB47,RNF40,RNASE11,HSPA4L,NQO2,CSF3,MGLL,GLIS1,NANOG,AK5,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,DRGX,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,SDHAF3,RNASE9,ZNF319,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,GXYLT2,SULF2,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,TSPAN18,FNDC3B,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,SFT2D1,CATIP,CDC42BPB,DNMT3A,CTSH,TSPAN3,PPM1M,ZNF385C,PRPSAP1,OTUD6B,HAVCR2,IQCG,CTNNBIP1,PDGFD,SLC37A2,ARMC9,NDUFA10,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,GLT1D1,LMF1,TM9SF4,HLA-DMB,SLCO2A1,KIAA1549,RAB31,ADK,SETD1A,RGSL1,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,ADPGK,TNIP3,SMAD1,GPRIN3,GPR161,TVP23A,RGS12,MFGE8,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,SLC6A6,DGKI,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,DIP2C,ABCC2,MBP,ELOVL3,CACHD1,RNF216,USP47,PPP1R13B,ANO10,SCYL2,AP3M2,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,LYPD8,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,BPIFB1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## [1] 1563    8
write.table(gem, file=file.path(res.dir, 
        paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hyper_", timeStamp, ".txt")),
            sep="\t", quote=F, row.names=F)

table(gem$Domain)
## 
## CORUM GO:BP GO:CC GO:MF    HP   HPA  KEGG MIRNA  REAC    WP 
##     1   584   161    93   296   351    10    42    20     5
path.hyper <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hyper)
## [1] 35  8
#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hyper, filter = 'top')
enrich.hypo <- gprofiler2::gost(query=uniq.hypo, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))
## Detected custom background input, domain scope is set to 'custom'
# for results containing all annotated terms
gem <- enrich.hypo$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)
##             GO.ID                        Description term_size
## 3776 MIRNA:000000                         MIRNA root     14165
## 1824   GO:0005515                    protein binding     13924
## 1825   GO:0005488                            binding     15946
## 1826   GO:0003674                 molecular_function     17356
## 1561   GO:0005622 intracellular anatomical structure     13844
## 1562   GO:0005737                          cytoplasm     11268
##      intersection_size Domain           FDR Phenotype
## 3776              2667  MIRNA 1.480722e-154        +1
## 1824              2578  GO:MF 1.904534e-125        +1
## 1825              2813  GO:MF 1.904534e-125        +1
## 1826              2959  GO:MF 2.615815e-125        +1
## 1561              2545  GO:CC 3.977935e-115        +1
## 1562              2203  GO:CC 5.258750e-113        +1
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Genes
## 3776                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,TTC7A,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,NHLRC4,KIAA1522,GNB5,TMED3,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,TNIK,TRIM9,DAPK2,TFF2,GFOD1,IL5RA,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,IL4,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,PNN,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CBFB,EPHB2,TTYH3,CHP1,VPS53,ZNF48,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,C6orf132,ERMAP,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,ITGAL,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,GALNT10,NVL,TPST1,POR,AXIN1,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,CCDC127,HK2,DYRK1A,MLX,BATF2,DAG1,KRT8,LGALS8,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,PLXNA2,ANKRD52,SERINC5,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,WWP2,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,BACH1,MAP6D1,C11orf24,DPH7,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,SPNS3,MAP1LC3B2,BDH1,FHL2,CMBL,RALGDS,NUTF2,TANGO2,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,SLC41A1,FOXJ3,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,AQP1,GPR156,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,FBXO7,ABCB9,CCDC85C,GRAMD1B,CALML4,PELI2,PHLDB3,SIAH2,MICAL2,MYLK,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,AMZ2,ZNF70,IL13,CCNY,DMAP1,SLC23A2,PRX,RREB1,ERGIC1,TMEM154,ABCC4,ADAMTS14,PDE4B,GNG12,PI4KA,NADK,ZC3H11A,SLC12A4,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,ZKSCAN5,RBL2,GSN,TRAF3,LTBP4,SEMA3B,MFAP4,TPCN1,MCM2,CAB39,GALM,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,PPP1R16B,NCK2,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,PTGDR2,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,XYLT1,CD86,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,UNC5B,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,WNT3,GALNT7,UXS1,MTUS2,DHCR24,PHF13,C19orf54,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,CDKN2AIPNL,WDFY2,RNF216,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,PHTF2,LARP1,TBC1D9B,CACNA1D,KBTBD4,CHRNE,LRRC8C,P2RX7,SLC11A1,PIK3AP1,LINC00548,P3H2,C1QTNF1,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,NBPF8,STON1-GTF2A1L,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,JAG1,XAF1,DNHD1,ERG,IMPA2,VAMP1,AGXT,NAP1L4,GTPBP1,CLDN10,VGLL4,GTSF1L,GON4L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,ZDHHC18,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,ACAD10,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,FAM135B,ITPRIP,DCAKD,IL18BP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,COL4A1,ARL15,SELPLG,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,PRNP,RHBDD2,C16orf70,SPATA21,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,MIDN,VEGFB,B3GALNT2,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,PDZD8,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,SUSD6,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,ITGA2,OPA3,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,ADCY9,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,PTPN1,B4GALT7,AAK1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,KIAA0232,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,SLC7A7,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,ZNFX1,ARSB,FBXL13,IP6K2,GRB2,EMC1,FOXN3,TAOK2,MCPH1,POC1A,LAX1,GPR35,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ZSWIM4,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,TMEM156,CDX1,DHX37,MVB12A,CLK3,TBC1D2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,CHST11,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PLD5,PADI2,KCNIP2,SIL1,LSM14A,INSC,LFNG,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,OPALIN,ERI3,SLC35D1,RNF24,CD4,TLE4,TTC17,USPL1,DNMT3A,RBM33,MACF1,SRF,ZBTB34,TMED10,LGR6,AACS,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ERAP2,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,IL1RN,PLEKHA7,SLC39A2,OAF,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,NHSL1,HECW2,SERF2,UGGT1,EXD2,SMG5,EARS2,SF3A1,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,TBXAS1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,RASSF5,ATXN1,TMEM41A,ARID5B,HDAC9,SLC44A4,TMCC2,ARFGAP2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,SLC25A45,MBNL2,ADORA2A-AS1,MCCC2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,BCL9,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,NMUR1,HIF1A,SAG,ILKAP,TNRC18,HIVEP2,EIF4EBP1,FAM107B,EEF2K,TRPM4,TMEM131,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,ART3,PDE4DIP,CPD,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,HMGXB4,SLMAP,PTP4A2,CCDC136,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TMEM220,AKR1E2,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,MAP3K14,BANK1,SART1,WDR70,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,LONRF2,MAML3,NR1H3,GZF1,MTA3,NIN,GOLGA3,HNRNPLL,ARRDC2,WDR8,TMEM241,MED15,PRG3,CARD11,HECTD4,RASSF4,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,HAVCR1,SCOC,ZNF563,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,CRISPLD2,CCDC50,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,EPHX4,NT5E,UST,ZRANB1,OSBPL6,TRIM71,EFR3A,SLC39A3,SRPK1,BEND6,RBM14,AGER,NANS,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,ZZEF1,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,DDX27,LDB2,DMXL1,ATXN7L1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,KLHL29,USP39,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,SUSD1,PHF1,HSD17B12,SIRPG,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,ARID4A,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,SPTBN2,SCN4A,ARHGAP10,HLCS,PEX2,STX2,KLHDC7A,L3MBTL1,IDO1,NAA16,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,FYN,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,ABTB2,MED13L,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,ZC3H7A,RNF13,EPAS1,CPM,PER2,ASAP2,WWC2,ERMN,ARL6IP6,TRPM3,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,RAB19,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TMEM17,TIGD1,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,SIGLEC10,CEP128,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,CACNB2,COL4A3BP,IDNK,TAF6,MAP4,DNAH3,ARHGAP12,RMDN3,EFCAB5,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,SEC62,PRIM2,THAP4,YARS,SUSD4,RASSF1,SLC35C1,IGF2BP2,SENP7,CRB1,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,ZFYVE21,LAPTM4A,FADS1,RALGPS1,SRP68,DBNL,PLA2G4F,MAST2,PHF21A,CRTAM,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,H6PD,AFF3,RIOK2,OR6B1,CDK2,CYSTM1,CHPT1,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,SNX10,ANTXR2,YWHAE,PHACTR2,WDR1,AKT3,JAZF1,SDC1,DNAJB13,PTH2R,TLE1,OLA1,CACFD1,SLC12A6,GNAI2,YES1,EXOC6B,TSPAN33,EREG,GPC5,RBM19,CPPED1,SMPD3,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ARHGEF3,C2CD3,DOCK4,TOLLIP,IKBKB,PSMD13,C12orf76,TPPP3,FER,KLF7,FANCA,PDE6B,SNUPN,SETBP1,MRPL10,ZCCHC14,STUB1,RDH5,CDK19,CES4A,CYTL1,IGSF3,CAPZA2,PHC3,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,MAML2,SETD2,PTPRN2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,FUT4,URGCP-MRPS24,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,NUP210,OTOF,FAM118A,TGFBRAP1,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,ZC3H4,MAPKAPK2,ORC1,TM7SF3,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,CBY3,RBM34,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,ASAH2B,ZCCHC24,CLCN6,NME2,CD300LB,VTI1B,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SLC7A6OS,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,FAM89A,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,ECHDC3,KLHL3,ADK,TMEM99,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ACADL,PARD3B,MYO1H,EPSTI1,PNRC1,PRKG2,CSNK1G3,FAM110B,TMEM117,KHDRBS3,EDEM2,SCARF2,XPC,GNA13,ABCG8,ALDH1A2,MYOM1,HNF4A,ISM2,KANK1,PLCXD2,WNT3A,TTC28,UBAP1,KRT6B,NR6A1,CXXC5,RNF121,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,NUGGC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SP110,TP53BP1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,MDFIC,CCND3,FTO,MARK2,ATP10B,GPR183,CLPB,LCORL,FAM168B,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,EFNA5,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,BATF,GEMIN5,RDM1,MYO1A,SLC39A1,RHBDD1,FAM207A,FCRLB,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,TMEM245,ITGB5,MNDA,ZNF507,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,PPRC1,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,PNPLA2,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,MCF2L2,DCTN5,MFSD12,TAF5L,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,C10orf105,ZKSCAN3,NDUFA4,ATP6V0A2,PIEZO1,ALPK3,SAMD8,MT2A,SMYD4,CLEC16A,HIBADH,MX1,TRAK2,CKS2,FURIN,UNK,YDJC,WWP1,GTF2F2,MRC2,SLC25A13,SNTB1,RAB7L1,FRYL,DRAP1,ARPC4,SLC13A4,SLC16A3,RPA1,FANCC,HCRTR1,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,BAHCC1,PEX11A,ECM2,ACSL6,STARD10,POPDC2,MYCT1,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,UBE2K,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,ZFC3H1,LYRM1,EHD4,PTPRF,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,RNF145,DCUN1D1,GREB1L,ZBTB7A,USP46,DHRS4,MYO5A,FAM174B,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,SHANK2,NFIL3,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,KCNK6,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,KCNK10,SLC16A10,STK24,ENPP2,BET1L,CCDC74B,ANKRD6,GPR132,FLT3,WDR37,PM20D2,LRP4,ZNF638,SLC30A1,RRBP1,GLUL,TTC22,ANKS6,FAM117A,PIGR,MATN1,AKIRIN1,HRH2,PDE7A,ETV3,TRAPPC12,DHX8,APOLD1,NRXN3,VRK1,PARP16,EDARADD,RSPRY1,ART4,NLK,FSTL4,SLC38A10,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,TLL2,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CABLES1,SCAF8,DCLK3,PRPF38B,IL18RAP,BUD31,UTRN,CSRP2BP,RFC4,ATP2A2,STK11IP,FRY,MDN1,AKT2,PRDX3,KLRK1,ANKH,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,CRIM1,SNRNP70,TRIM2,ZNF552,TRAM2,DCBLD1,FNIP1,TP53BP2,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,KNDC1,JDP2,RALGPS2,ARSK,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,SGPP1,PARP1,NCAPD2,ZBTB38,SLC4A8,ACTRT2,CYBRD1,NTAN1,MEGF11,MFF,LRRC42,ITGB4,TRPM7,FRMD4B,CDH18,TMEM79,SLC37A1,PRDM2,CAT,OSBPL10,FBXW7,MERTK,LILRA1,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,PLXNC1,NR1I2,LRFN1,RUNX1,SNX4,TACR2,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,TMEM64,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,RNF130,ARHGEF10L,LRRFIP2,ZNF333,AAR2,PLA2G4A,CA12,ATG16L1,CMTM7,MTA1,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,HAL,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,ACP6,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,IL1RAP,ATXN7,PEX14,PDE4C,ALPK2,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,GULP1,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,NCOA2,ACTB,PIGC,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,ST3GAL5,SMPDL3A,ATG10,COPA,ARHGAP9,DNAJC5,CEP83,CSNK1G2,RPS15A,ASB2,TRABD,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,PCNA,DHRS11,LETM1,LPIN2,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,C1RL,MPPED1,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,MAP2K6,CREB3L1,FBXO9,IL10RA,LRCH3,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ADIPOR1,NDUFS6,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,ATL1,PAX7,ZMIZ1,DRD2,CD47,EFR3B,TMEM184B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ZNF652,PLAA,IL15,ARNT,NEURL1B,SERPINF1,SLC25A10,TMEM45B,TMEM168,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,BRD7,ATAD3C,MIA3,GMPPB,A2ML1,ARID4B,PFKFB4,C1orf122,CEP295,ALOX5,EHMT2,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,PEAK1,FLOT1,CAND2,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,CNKSR3,LOC81691,WIZ,ZDHHC14,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,KPNB1,KCNN3,KRI1,CLPTM1,B3GALNT1,NUDT19,GPRC5A,CDH22,ALDH6A1,GALNT11,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,EDEM3,PROK2,CARS,ARMC2,RAB8B,CHST3,RAP1A,TNPO1,MTF1,RASGRP3,PSEN1,MRPL16,SGSM2,SMYD5,P2RY6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,GMDS,PGS1,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,DEFB125,BTN3A3,ALG14,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,ELP6,PRPF8,PACS2,MON2,ALAD,PANK1,CCDC146,RPS6KA1,NEK1,NMNAT1,GTDC1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,CACHD1,ZFAND6,RASA2,RB1CC1,DFFA,PKNOX1,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,GCNT3,ZNF565,C1orf9,PRKAR2A,ZNF740,PCM1,RNASET2,MTMR7,TRPM5,TNFRSF13C,ZNF518B,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,MARK4,C9orf64,DHX33,PIK3R3,ASB3,JADE2,MAP3K5,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,SORBS1,PIKFYVE,CAMK4,KIAA1549,DDA1
## 1824                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,TRIO,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,TESC,USP32,TRPC4AP,IGF1R,TRAPPC9,UVRAG,MUC13,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GNAO1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,TPST1,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,WWP2,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ABR,DOCK1,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,RALGDS,NUTF2,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,GLYR1,SLC18A2,DPPA3,SLC41A1,FOXJ3,CLRN1,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,FBXO7,ABCB9,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,MYLK,ADTRP,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,ZNF789,PRX,ERGIC1,TMEM154,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,MFAP4,TPCN1,MCM2,KEL,CAB39,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,TNN,PPP1R16B,NCK2,IKZF1,HECW1,MAML1,SLC29A3,GSTM3,TGFA,CEBPB,STK3,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,CD86,SOAT2,FMO1,MAN1C1,RAP1GAP2,MED12L,UNC5B,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,KAT8,WNT3,UXS1,MTUS2,DHCR24,CDH23,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,TTLL6,NELFCD,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,CD7,LARP1,TBC1D9B,CACNA1D,KBTBD4,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,C1QTNF1,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,CALR3,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,HK1,RIN3,SLC7A11,MLST8,JAG1,ST7,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,HPX,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,HVCN1,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,SLIT3,USP19,ITPRIP,IL18BP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,DGKI,NLRC5,RBX1,THRB,SGSM3,TGFB3,EIF6,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,HDC,PRNP,RHBDD2,C16orf70,IQCD,DHX30,PRDM10,THG1L,KRT72,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,C16orf45,FCGR2A,ENO3,SUSD6,ZNF699,GDF5,RBPMS,RASGRP1,ITGA2,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,FBF1,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,RALY,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,RNF43,EHBP1,HPS4,CHCHD3,VEPH1,CLEC4C,FBXL13,IP6K2,GRB2,FOXN3,TAOK2,MCPH1,POC1A,LAX1,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,CDX1,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,ATP1A4,LGALS12,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,MACF1,TYW1B,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,SVOPL,P4HB,MICAL1,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,SHF,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,ANKRD35,HECW2,UGT1A8,UGGT1,EXD2,SMG5,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,BBS1,DLGAP1,RASSF5,ATXN1,TMEM41A,ARID5B,CLTCL1,HDAC9,TMCC2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,C7orf50,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,OXER1,BCL9,CHMP1A,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,SKI,KCNE1,PPM1A,HIF1A,SAG,SLC14A2,DOCK2,ILKAP,EIF4EBP1,EEF2K,TRPM4,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,LHPP,TXNRD2,MUC20,TMEM220,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,BANK1,SART1,WDR70,MEGF10,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,LONRF2,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,CLCN1,MED15,CARD11,RYR1,RASSF4,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,SMIM22,SCOC,ZNF563,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CCDC50,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,SLC39A7,TOR2A,EPHX4,NT5E,ZRANB1,OSBPL6,TRIM71,SLC39A3,SRPK1,RBM14,AGER,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,CTDSPL,PAM16,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,PLA2G6,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,APOL3,LDB2,SPATA24,DMXL1,ATXN7L1,STAT4,TRAF1,F5,MAPK1,KLHL29,USP39,TTC23,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,PHF1,HSD17B12,SIRPG,PMM1,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,ARAP1,POLR1A,N4BP2L2,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,NOTCH2,SEPHS1,CYB5R3,SMURF2,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,CCL23,CRYBB1,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,SCN4A,ARHGAP10,HLCS,ECT2L,PEX2,FARP2,STX2,KLHDC7A,L3MBTL1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,SETMAR,FYN,RBKS,UPF1,ADAP1,THEMIS2,ABTB2,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,PER2,ASAP2,WWC2,ERMN,PROK1,ARL6IP6,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,PPP2R5B,RAB19,CLMN,STAT3,SLAMF1,MEF2C,MAP4K5,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,TMEM17,TIGD1,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,SIGLEC10,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,CACNB2,COL4A3BP,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,FTL,PRDM16,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,PRIM2,THAP4,YARS,SUSD4,RASSF1,IGF2BP2,SENP7,CRB1,AUTS2,XPO6,RUNX3,PDXDC1,CLK2,ZFYVE21,LAPTM4A,HBZ,RALGPS1,SRP68,DBNL,ADORA1,MAST2,PHF21A,CRTAM,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,RIOK2,OR6B1,NTRK1,CDK2,CYSTM1,CHPT1,C22orf15,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SEMA4A,SDC1,DNAJB13,PTH2R,TLE1,OLA1,CACFD1,GSAP,SLC12A6,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,TMPRSS9,GPC5,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,TPPP3,FER,FANCA,PDE6B,EBF3,SNUPN,DRC7,CHID1,SETBP1,MRPL10,CAPN10,ZCCHC14,STUB1,RDH5,CYTL1,CAPZA2,PHC3,CCDC167,KAT5,CEP85,SIPA1L2,SETD2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,FSCN3,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,UCKL1,FAM118A,TGFBRAP1,DHRS7,IRF2,TIMM22,GSK3B,YWHAZ,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,MAPKAPK2,ORC1,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,NME2,VTI1B,MRAP,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,SIGLEC7,ATP1A1,CTLA4,FAH,TAGAP,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,KLHL3,IGF2R,CRTC1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MCF2L,MYO10,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ADGRA3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,EPSTI1,PNRC1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,KHDRBS3,DAPP1,ZNF438,SCARF2,XPC,GNA13,ABCG8,MYOM1,HNF4A,ISM2,KANK1,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,FCRL3,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CCDC86,RPL36AL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SPATA25,SP110,TP53BP1,ANGPT1,ASPSCR1,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,CLPB,LCORL,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,RASAL2,COG7,NDUFV2,EFNA5,CDH15,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,PILRA,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,ITGB5,MNDA,BTBD11,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,RAB11FIP3,PPRC1,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,RSU1,NFE2,DCTN5,MFSD12,TAF5L,ITGB7,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,CCDC183,PIEZO1,SYCE2,SAMD8,MT2A,SMYD4,HIBADH,MX1,TRAK2,CKS2,FURIN,WWP1,GTF2F2,MRC2,SLC25A13,UGT1A7,SNTB1,SLC38A11,RAB7L1,FRYL,DRAP1,ARPC4,SLC13A4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,PEX11A,INPP1,ECM2,ACSL6,STARD10,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,GNA14,NUSAP1,GJA4,ZFC3H1,EHD4,PTPRF,LMO4,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,FAM81B,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,ASL,SHANK2,NFIL3,THRSP,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,SLC16A10,STK24,ENPP2,CCDC74B,ANKRD6,FLT3,WDR37,PM20D2,LRP4,SLC30A1,ALKBH2,GLUL,TTC22,ANKS6,MATN1,AKIRIN1,ETV3,TRAPPC12,DHX8,SLC8B1,NRXN3,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,PPIC,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CSF3R,CABLES1,SCAF8,IL18RAP,BUD31,UTRN,RFC4,ATP2A2,STK11IP,MDN1,AKT2,ARMC4,PRDX3,MAP4K1,KLRK1,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,OSGIN1,PARP10,ZNF131,MCFD2,CCDC141,NEIL2,FGF18,CD58,CRIM1,SNRNP70,TRIM2,ZNF552,RTP2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,IVNS1ABP,JDP2,RALGPS2,NRXN2,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,PARP1,NCAPD2,TTBK2,ZBTB38,CYBRD1,NTAN1,FARS2,MEGF11,MFF,LRRC42,SPPL2B,ITGB4,TRPM7,CDH18,TMEM79,ARMC9,PRDM2,WFDC5,CAT,OSBPL10,FBXW7,MERTK,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,ADAM11,PLXNC1,NR1I2,LRFN1,RUNX1,UBASH3A,SNX4,TACR2,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,HPSE2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,CPB1,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,ARHGEF10L,LRRFIP2,HYAL2,ATG16L1,CMTM7,ICA1,MTA1,PADI6,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,KCNA10,IL1RAP,ATXN7,PHF2,PEX14,PDE4C,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,METTL1,LTC4S,CASKIN2,PPTC7,CARD14,ALS2,DTNA,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,ZGPAT,NCOA2,ACTB,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,SMPDL3A,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,EPHA10,PCNA,DHRS11,LETM1,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,GIPR,IL10RA,LRCH3,DNAJC4,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,ADIPOR1,RABGAP1L,PKD2,ZNF704,USP1,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,NCR2,SERPINF1,SLC25A10,TMEM45B,PGAP2,JPH2,DNAJC13,RAB27A,CREB3L3,BRD7,MIA3,TRIM62,ZP1,GMPPB,A2ML1,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,GNA15,CNKSR3,WIZ,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,CLPTM1,GPRC5A,CDH22,GALNT11,FAM149B1,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,PROK2,CARS,ARMC2,RAB8B,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,SGSM2,SMYD5,P2RY6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,GRM2,PPP1CA,INTS8,SEC63,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,KLHL5,GPS2,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,MMP28,GMDS,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,BTN3A3,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,CD6,HBS1L,ANKRD9,NCAM1,ATF6,PDPK1,MAP2K3,PLCB1,ADD3,CD84,BIK,NUCKS1,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,ESYT2,SLC40A1,ZFAND6,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,PRKAR2A,ZNF740,RSPH14,PCM1,MTMR7,TRPM5,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,PCOLCE,MARK4,C9orf152,C9orf64,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1825                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,ABCC1,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,GNAO1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,TPST1,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,WWP2,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,RALGDS,NUTF2,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,POLR2F,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,FOXJ3,CLRN1,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,MYLK,ADTRP,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,AMZ2,ZNF70,IL13,CCNY,DMAP1,ZNF789,PRX,RREB1,ERGIC1,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,MFAP4,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,TNN,PPP1R16B,NCK2,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,PTGDR2,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,XYLT1,CD86,SOAT2,FMO1,MAN1C1,METTL16,RAP1GAP2,MED12L,UNC5B,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,ZNF532,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,KAT8,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,CD7,LARP1,TBC1D9B,CACNA1D,KBTBD4,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,C1QTNF1,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,CALR3,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,HK1,RIN3,SLC7A11,MLST8,JAG1,ST7,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,HPX,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,PAFAH2,SLIT3,USP19,ITPRIP,DCAKD,IL18BP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,SEC14L2,NAPA,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,HDC,PRNP,RHBDD2,C16orf70,SPATA21,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,ENO3,SUSD6,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,ITGA2,FTCDNL1,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,ADCY9,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,KIAA0232,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,VEPH1,ZNFX1,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,FOXN3,TAOK2,MCPH1,POC1A,LAX1,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ZSWIM4,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,CDX1,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,P4HTM,DGKG,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,ATP1A4,LFNG,LGALS12,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,ERI3,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,RBM33,MACF1,TYW1B,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,SVOPL,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,SHF,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,ANKRD35,HECW2,UGT1A8,UGGT1,EXD2,SMG5,EARS2,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,TBXAS1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,DLGAP1,RASSF5,ATXN1,TMEM41A,ARID5B,CLTCL1,HDAC9,TMCC2,ARFGAP2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,C7orf50,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,OXER1,BCL9,CHMP1A,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,SKI,KCNE1,PPM1A,NMUR1,HIF1A,SAG,SLC14A2,DOCK2,ILKAP,TNRC18,HIVEP2,EIF4EBP1,EEF2K,TRPM4,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,CPD,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TMEM220,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,BANK1,SART1,WDR70,MEGF10,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,LONRF2,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,CLCN1,MED15,PRG3,CARD11,RYR1,RASSF4,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,SMIM22,HAVCR1,SCOC,ZNF563,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,EPHX4,NT5E,ZRANB1,OSBPL6,TRIM71,SLC39A3,SRPK1,BEND6,RBM14,AGER,MIR101-2,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,ZZEF1,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,PLA2G6,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,DDX27,APOL3,LDB2,SPATA24,DMXL1,ATXN7L1,GALNTL6,STAT4,TRAF1,F5,MAPK1,KLHL29,USP39,TTC23,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,SUSD1,PHF1,HSD17B12,SIRPG,PMM1,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,CCL23,ARID4A,CRYBB1,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,SCN4A,ARHGAP10,HLCS,ECT2L,PEX2,FARP2,STX2,KLHDC7A,L3MBTL1,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,SETMAR,FYN,RBKS,UPF1,ADAP1,POLR3A,THEMIS2,ABTB2,ANKRD11,SPOP,LRIT3,TSNAX-DISC1,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,CPM,PER2,ASAP2,WWC2,ERMN,PROK1,ARL6IP6,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,PPP2R5B,RAB19,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TMEM17,TIGD1,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,SIGLEC10,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,CACNB2,COL4A3BP,IDNK,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,EFCAB5,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,PRIM2,THAP4,YARS,SUSD4,RASSF1,CSAD,IGF2BP2,SENP7,CRB1,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,CLK2,ACOXL,ZFYVE21,LAPTM4A,HBZ,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,PHF21A,CRTAM,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,DPEP2,H6PD,AFF3,RIOK2,OR6B1,NTRK1,CDK2,CYSTM1,CHPT1,C22orf15,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SEMA4A,SDC1,DNAJB13,PTH2R,TLE1,PLA2G15,OLA1,CACFD1,GSAP,MIR3909,SLC12A6,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,TMPRSS9,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,TPPP3,FER,KLF7,FANCA,PDE6B,EBF3,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,ZCCHC14,ULK4,STUB1,RDH5,CDK19,CYTL1,CAPZA2,PHC3,CCDC167,ENTPD7,KAT5,CEP85,SIPA1L2,SETD2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,FSCN3,CDCA7,PARN,COL1A1,CLCNKB,ATF7,SEC23B,TRAPPC3,UCKL1,OTOF,FAM118A,TGFBRAP1,DHRS7,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,ZC3H4,MAPKAPK2,ORC1,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,RBM34,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,ZCCHC24,CLCN6,NME2,VTI1B,MRAP,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,SIGLEC7,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ADGRA3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,EPSTI1,PNRC1,SLFNL1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,KHDRBS3,DAPP1,ZNF438,EDEM2,SCARF2,XPC,GNA13,ABCG8,ALDH1A2,MYOM1,HNF4A,ISM2,KANK1,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,FCRL3,NUGGC,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,GDPD3,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SPATA25,SP110,TP53BP1,ANGPT1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,GPR183,CLPB,LCORL,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,NDUFV2,EFNA5,CDH15,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,PILRA,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,ITGB5,MNDA,ZNF507,BTBD11,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,RAB11FIP3,PPRC1,ACSM6,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,NFE2,DCTN5,MFSD12,TAF5L,ITGB7,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,CCDC183,PIEZO1,SYCE2,ALPK3,SAMD8,MT2A,SMYD4,HIBADH,MX1,TRAK2,CKS2,FURIN,UNK,YDJC,WWP1,GTF2F2,MRC2,SLC25A13,UGT1A7,SNTB1,SLC38A11,RAB7L1,FRYL,DRAP1,ARPC4,LTB4R,SLC13A4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,HCRTR1,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,BAHCC1,PEX11A,INPP1,ECM2,ACSL6,STARD10,POPDC2,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,GJA4,ZFC3H1,EHD4,PTPRF,LMO4,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,ASL,SHANK2,NFIL3,THRSP,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,SLC16A10,STK24,ENPP2,CCDC74B,ANKRD6,FLT3,WDR37,PM20D2,LRP4,ZNF638,SLC30A1,ALKBH2,RRBP1,GLUL,TTC22,ANKS6,MATN1,AKIRIN1,PDE7A,ETV3,TRAPPC12,SLC27A3,DHX8,SLC8B1,APOLD1,NRXN3,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,TLL2,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CSF3R,CABLES1,SCAF8,DCLK3,PRPF38B,IL18RAP,BUD31,UTRN,RFC4,ATP2A2,STK11IP,MDN1,AKT2,ARMC4,PRDX3,MAP4K1,KLRK1,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,OSGIN1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,CRIM1,SNRNP70,TRIM2,ZNF552,RTP2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,JDP2,RALGPS2,ARSK,NRXN2,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,PARP1,NCAPD2,TTBK2,ZBTB38,CYBRD1,NTAN1,FARS2,MEGF11,MFF,LRRC42,SPPL2B,ITGB4,TRPM7,CDH18,TMEM79,ARMC9,PRDM2,WFDC5,CAT,OSBPL10,FBXW7,MERTK,LILRA1,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,ADAM11,PLXNC1,NR1I2,LRFN1,RUNX1,UBASH3A,SNX4,TACR2,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,HPSE2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,CPB1,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,LRRFIP2,ZNF333,PLA2G4A,HYAL2,CA12,ATG16L1,CMTM7,ICA1,MTA1,PADI6,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,KCNA10,IL1RAP,ATXN7,PHF2,PEX14,PDE4C,ALPK2,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,A3GALT2,ZGPAT,NCOA2,ACTB,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,SMPDL3A,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,EPHA10,PCNA,DHRS11,LETM1,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,GIPR,IL10RA,LRCH3,DNAJC4,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,ADIPOR1,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,NCR2,SERPINF1,SLC25A10,TMEM45B,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,ZP1,GMPPB,A2ML1,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MGAM2,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,GNA15,CNKSR3,LOC81691,WIZ,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,CLPTM1,NUDT19,GPRC5A,CDH22,ALDH6A1,GALNT11,FAM149B1,CDYL,ACVR2A,RNF224,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,EDEM3,PROK2,CARS,ARMC2,RAB8B,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,SMYD5,P2RY6,FER1L6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,GRM2,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,GPS2,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,BTN3A3,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,CD6,HBS1L,ANKRD9,NCAM1,ATF6,PDPK1,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,ZNF565,PRKAR2A,ZNF740,RSPH14,PCM1,RNASET2,MTMR7,TRPM5,ZNF518B,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,PCOLCE,MARK4,C9orf152,C9orf64,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1826 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,SLC4A5,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,TTYH3,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,GNAO1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,TPST1,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,WWP2,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,SPNS3,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,RALGDS,NUTF2,CCL18,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,FOXJ3,CLRN1,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,GPR156,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,MYLK,ADTRP,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,AMZ2,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,PRX,RREB1,ERGIC1,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,MFAP4,CCDC182,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,TNN,PPP1R16B,NCK2,ST3GAL4,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,PTGDR2,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,CD86,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,UNC5B,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,KAT8,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,ELL3,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,CD7,LARP1,TBC1D9B,CACNA1D,KBTBD4,CHRNE,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,C1QTNF1,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,CALR3,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,JAG1,ST7,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,PIGL,NPL,GTPBP1,HPX,CLDN10,VGLL4,GTSF1L,GON4L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,ZDHHC18,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,ITPRIP,DCAKD,IL18BP,SREBF2,ASIC1,TMIGD3,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,SEC14L2,NAPA,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,HDC,PRNP,RHBDD2,C16orf70,SPATA21,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,HNMT,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,ENO3,SUSD6,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,ITGA2,FTCDNL1,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,ADCY9,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,KIAA0232,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,SLC7A7,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,VEPH1,ZNFX1,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,EMC1,FOXN3,TAOK2,MCPH1,POC1A,LAX1,GPR35,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ZSWIM4,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,CDX1,DHX37,MVB12A,CLK3,TBC1D2,CPVL,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,CHST11,P4HTM,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PLD5,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,ATP1A4,LFNG,LGALS12,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,ERI3,SLC35D1,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,RBM33,MACF1,TYW1B,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,SVOPL,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,SHF,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,ANKRD35,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,TBXAS1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,DLGAP1,RASSF5,ATXN1,TMEM41A,ARID5B,CLTCL1,HDAC9,SLC44A4,TMCC2,ARFGAP2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,SLC25A45,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,C7orf50,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,OXER1,BCL9,CHMP1A,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,NMUR1,HIF1A,SAG,SLC14A2,DOCK2,ILKAP,TNRC18,HIVEP2,EIF4EBP1,RGS9,EEF2K,TRPM4,TMEM131,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,ART3,PDE4DIP,CPD,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TMEM220,AKR1E2,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,BANK1,SART1,WDR70,MEGF10,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,LONRF2,MAML3,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,CLCN1,MED15,PRG3,CARD11,RYR1,HECTD4,RASSF4,MFSD2B,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,SMIM22,HAVCR1,SCOC,ZNF563,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,EPHX4,NT5E,UST,ZRANB1,OSBPL6,TRIM71,SLC39A3,SRPK1,BEND6,RBM14,AGER,NANS,MIR101-2,PLB1,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,ZZEF1,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,PLA2G6,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,DDX27,APOL3,LDB2,SPATA24,DMXL1,ATXN7L1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,KLHL29,USP39,TTC23,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,SUSD1,PHF1,HSD17B12,SIRPG,PMM1,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,OR52B6,CCL23,ARID4A,CRYBB1,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,SCN4A,ARHGAP10,HLCS,ECT2L,PEX2,FARP2,STX2,KLHDC7A,L3MBTL1,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,SETMAR,FYN,RBKS,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,ABTB2,MED13L,ANKRD11,SPOP,LRIT3,TSNAX-DISC1,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,CPM,PER2,ASAP2,WWC2,ERMN,PROK1,ARL6IP6,TRPM3,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,PPP2R5B,RAB19,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TMEM17,TIGD1,CXCR4,TMEM201,OR2B2,DAZAP1,PGM1,IMMT,SIGLEC10,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,CACNB2,COL4A3BP,IDNK,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,EFCAB5,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,SEC62,PRIM2,THAP4,YARS,SUSD4,RASSF1,CSAD,SLC35C1,IGF2BP2,SENP7,CRB1,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,CLK2,ACOXL,ZFYVE21,LAPTM4A,HBZ,FADS1,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,PHF21A,CRTAM,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,DPEP2,H6PD,AFF3,RIOK2,OR6B1,NTRK1,CDK2,CYSTM1,CHPT1,C22orf15,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SEMA4A,SDC1,DNAJB13,PTH2R,TLE1,PLA2G15,OLA1,CACFD1,GSAP,MIR3909,SLC12A6,GNAI2,YES1,OR6M1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,TMPRSS9,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,PSMD13,TPPP3,FER,KLF7,FANCA,PDE6B,EBF3,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,ZCCHC14,ULK4,STUB1,RDH5,CDK19,CES4A,CYTL1,IGSF3,CAPZA2,PHC3,CCDC167,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,MAML2,SETD2,PTPRN2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,FUT4,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,FSCN3,CDCA7,PARN,COL1A1,CLCNKB,ATF7,SEC23B,TRAPPC3,UCKL1,OTOF,FAM118A,TGFBRAP1,DHRS7,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,ZC3H4,MAPKAPK2,ORC1,TM7SF3,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,RBM34,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,ASAH2B,ZCCHC24,CLCN6,NME2,CD300LB,VTI1B,MRAP,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,SIGLEC7,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,ECHDC3,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ADGRA3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,EPSTI1,PNRC1,SLFNL1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,TMEM117,KHDRBS3,DAPP1,ZNF438,EDEM2,SCARF2,XPC,GNA13,ABCG8,ALDH1A2,MYOM1,HNF4A,ISM2,KANK1,PLCXD2,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,FCRL3,NUGGC,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,TSPAN32,ATP8B1,SHROOM3,CCR3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,GDPD3,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SPATA25,SP110,TP53BP1,ANGPT1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,GPR183,CLPB,LCORL,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,NDUFV2,EFNA5,CDH15,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,SLC9C2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,PILRA,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,FCRLB,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,DEGS2,TMEM245,ITGB5,MNDA,ZNF507,BTBD11,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,PPRC1,ACSM6,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,PNPLA2,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,NFE2,MCF2L2,DCTN5,MFSD12,TAF5L,ITGB7,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,CCDC183,PIEZO1,SYCE2,ALPK3,SAMD8,MT2A,SMYD4,CLEC16A,HIBADH,MX1,TRAK2,CKS2,FURIN,UNK,YDJC,WWP1,GTF2F2,MRC2,SLC25A13,UGT1A7,SNTB1,SLC38A11,RAB7L1,FRYL,DRAP1,ARPC4,LTB4R,SLC13A4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,HCRTR1,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,BAHCC1,PEX11A,INPP1,ECM2,ACSL6,STARD10,POPDC2,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,GJA4,ZFC3H1,EHD4,PTPRF,LMO4,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,ASL,SHANK2,NFIL3,THRSP,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,KCNK6,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,KCNK10,SLC16A10,STK24,ENPP2,BET1L,CCDC74B,ANKRD6,GPR132,FLT3,WDR37,PM20D2,LRP4,ZNF638,SLC30A1,ALKBH2,RRBP1,GLUL,TTC22,ANKS6,PIGR,MATN1,AKIRIN1,HRH2,PDE7A,ETV3,TRAPPC12,SLC27A3,DHX8,SLC8B1,APOLD1,NRXN3,PIEZO2,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,ART4,NLK,FSTL4,PRKCQ,SLC38A10,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,TLL2,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CSF3R,CABLES1,SCAF8,DCLK3,PRPF38B,IL18RAP,BUD31,UTRN,RFC4,ATP2A2,STK11IP,FRY,MDN1,AKT2,ARMC4,PRDX3,MAP4K1,KLRK1,ANKH,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,OSGIN1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,CRIM1,SNRNP70,TRIM2,ZNF552,RTP2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,KNDC1,JDP2,RALGPS2,ARSK,NRXN2,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,SGPP1,PARP1,NCAPD2,TTBK2,ZBTB38,SLC4A8,CYBRD1,NTAN1,FARS2,MEGF11,MFF,LRRC42,SPPL2B,ITGB4,TRPM7,CDH18,TMEM79,SLC37A1,ARMC9,PRDM2,WFDC5,CAT,OSBPL10,FBXW7,MERTK,LILRA1,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,ADAM11,PLXNC1,NR1I2,LRFN1,RUNX1,UBASH3A,SNX4,TACR2,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,HPSE2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,CPB1,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,LRRFIP2,FKBP11,ZNF333,PLA2G4A,HYAL2,CA12,ATG16L1,OR10P1,CMTM7,ICA1,MTA1,PADI6,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,HAL,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,ACP6,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,KCNA10,IL1RAP,ATXN7,PHF2,PEX14,PDE4C,ALPK2,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,A3GALT2,ZGPAT,NCOA2,ACTB,PIGC,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,ST3GAL5,SMPDL3A,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,EPHA10,PCNA,DHRS11,LETM1,LPIN2,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,C1RL,MPPED1,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,GIPR,IL10RA,LRCH3,DNAJC4,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,ADIPOR1,NDUFS6,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,NCR2,SERPINF1,SLC25A10,TMEM45B,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,MRPL55,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,ZP1,GMPPB,A2ML1,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MGAM2,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,GNA15,CNKSR3,LOC81691,WIZ,ZDHHC14,ELF1,TSPAN14,STAU2,NFE2L1,OR2AE1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,CLPTM1,B3GALNT1,NUDT19,GPRC5A,CDH22,ALDH6A1,GALNT11,FAM149B1,CDYL,ACVR2A,RNF224,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,EDEM3,PROK2,CARS,ARMC2,RAB8B,CHST3,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,SMYD5,P2RY6,FER1L6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,GRM2,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,GPS2,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,BTN3A3,FKBP1B,MRPS14,PWP2,PRSS41,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,CD6,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,ELP6,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,GTDC1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,CACHD1,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,ST8SIA6,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,GCNT3,ZNF565,PRKAR2A,ZNF740,RSPH14,PCM1,RNASET2,MTMR7,TRPM5,TNFRSF13C,ZNF518B,OR6P1,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,PCOLCE,MARK4,C9orf152,NAGLU,C9orf64,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1561                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,GUSB,TCEA2,MSMP,GNB5,TMED3,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,MED25,ZBTB32,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,GNAO1,IRGC,TRIM33,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,TPST1,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,WWP2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,RALGDS,NUTF2,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,FOXJ3,CLRN1,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,PICALM,GNAQ,MAFK,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,MICAL2,MYLK,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,PRX,RREB1,HCFC1R1,ERGIC1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,PPP1R16B,NCK2,ST3GAL4,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,CD86,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,TLDC2,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,ZNF532,SIK3,EML3,SNX9,MCMBP,DNAJC3,KAT8,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,ATG13,NEK8,PHTF2,LARP1,CACNA1D,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,PIGL,NPL,GTPBP1,HPX,CLDN10,VGLL4,GON4L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,ASB8,ZDHHC18,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SND1,MBD6,RCC2,PAFAH2,SLIT3,USP19,ITPRIP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,WWOX,SEC14L2,NAPA,LEF1,OSBP2,RIBC2,HDC,PRNP,RHBDD2,C16orf70,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,HNMT,THADA,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,ENO3,XPR1,ZNF699,RBPMS,ARSG,RASGRP1,ITGA2,OPA3,HNRNPM,SIPA1L3,RMND1,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,ZNFX1,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,EMC1,FOXN3,TAOK2,MCPH1,POC1A,LAX1,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ERP29,ADAM19,PCCA,TBL2,STT3A,CDX1,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,CHST11,P4HTM,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,LFNG,LGALS12,GDPD5,MYO9B,DNAJC18,SUPT3H,PPP2R5C,OPALIN,SLC35D1,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,MACF1,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,MTFR1,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,MAPKAPK3,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SACS,C20orf203,MTHFD2,TBXAS1,CRTC3,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,RASSF5,ATXN1,ARID5B,CLTCL1,HDAC9,TMCC2,ARFGAP2,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,SLC25A45,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,UPP2,ARHGEF7,SYTL3,BCL9,CHMP1A,FAIM2,VDR,RAD21,CEBPE,SPECC1L-ADORA2A,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,HIF1A,SAG,DOCK2,ILKAP,TNRC18,HIVEP2,EIF4EBP1,RGS9,EEF2K,TRPM4,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,CCDC136,AGPS,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,SART1,WDR70,ZC3H7B,SLC25A3,PLAGL1,AP1M1,SLC2A5,ITGB3,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,MAML3,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,MED15,PRG3,CARD11,RYR1,MAK16,GAPVD1,EPB41L2,GAPT,POLR1C,GNAI1,NR3C1,NAA25,SMIM22,SCOC,ZNF563,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,NT5E,UST,ZRANB1,OSBPL6,TRIM71,EFR3A,SRPK1,BEND6,RBM14,AGER,NANS,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,FBXW11,MIEF2,LOXL1,OGDH,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SPPL3,EYA3,SDCCAG8,PLA2G6,BDKRB2,SNAP47,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,APOL3,LDB2,SPATA24,DMXL1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,USP39,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,PHF1,HSD17B12,PMM1,ZNF628,PTPRC,AP2B1,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,ADRBK2,ARID4A,PELI1,LIMD1,CHST15,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,ARHGAP10,HLCS,PEX2,FARP2,STX2,L3MBTL1,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,SETMAR,FYN,RBKS,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,MED13L,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,PER2,ASAP2,WWC2,ERMN,ARL6IP6,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,PPP2R5B,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TIGD1,CXCR4,TMEM201,FAM53A,DAZAP1,PGM1,IMMT,CEP128,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,COL4A3BP,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,APP,GPSM1,SEC62,PRIM2,YARS,RASSF1,CSAD,SLC35C1,IGF2BP2,SENP7,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,CLK2,ACOXL,ZFYVE21,LAPTM4A,HBZ,FADS1,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,PHF21A,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,TIMP2,RFFL,H6PD,AFF3,RIOK2,NTRK1,CDK2,CYSTM1,CHPT1,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,GGNBP2,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SDC1,DNAJB13,TLE1,PLA2G15,OLA1,GSAP,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,PSMD13,TPPP3,FER,KLF7,FANCA,EBF3,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,STUB1,RDH5,CDK19,CAPZA2,PHC3,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,MAML2,SETD2,PTPRN2,TALDO1,MFSD10,DEDD,FOXO3,CAPN7,FUT4,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,BSCL2,FSCN3,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,NUP210,UCKL1,OTOF,TGFBRAP1,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,GMEB1,ZC3H4,MAPKAPK2,ORC1,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,RBM34,PAX8,DPP9,CPNE2,MPV17,PALD1,CLCN6,NME2,VTI1B,MRAP,NPM3,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SLC7A6OS,SARM1,CSRNP2,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,ECHDC3,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,PNRC1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,TMEM117,KHDRBS3,DAPP1,ZNF438,EDEM2,XPC,GNA13,ALDH1A2,MYOM1,HNF4A,KANK1,PLCXD2,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,NUGGC,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,GDPD3,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SP110,TP53BP1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,CLPB,LCORL,FAM168B,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,UPF3A,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,NDUFV2,CDH15,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,CNPY3,XPNPEP3,SORBS2,PDZRN3,DCTN2,TPST2,SHPRH,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,FCRLB,FDFT1,PARP4,GLE1,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,DEGS2,ITGB5,MNDA,ZNF507,SERPINB6,TTLL4,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,PPRC1,ACSM6,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,PNPLA2,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,NFE2,DCTN5,MFSD12,TAF5L,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,PIEZO1,SYCE2,ALPK3,SAMD8,MT2A,CLEC16A,HIBADH,MX1,TRAK2,FURIN,UNK,WWP1,GTF2F2,SLC25A13,UGT1A7,SNTB1,RAB7L1,FRYL,DRAP1,ARPC4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,PEX11A,INPP1,ACSL6,STARD10,MYCT1,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,TGFBR2,TULP4,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,ZFC3H1,LYRM1,EHD4,LMO4,LEPROTL1,ITPR2,EXOC4,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FAM174B,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,EDRF1,TMEM130,ASL,SHANK2,NFIL3,THRSP,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,KIF13B,SLC16A10,STK24,BET1L,ANKRD6,FLT3,WDR37,PM20D2,ZNF638,SLC30A1,ALKBH2,RRBP1,GLUL,ANKS6,PIGR,AKIRIN1,PDE7A,ETV3,TRAPPC12,SLC27A3,DHX8,SLC8B1,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,SLC38A10,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,CABLES1,SCAF8,DCLK3,PRPF38B,BUD31,UTRN,CSRP2BP,RFC4,ATP2A2,STK11IP,FRY,MDN1,AKT2,ARMC4,PRDX3,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,SNRNP70,TRIM2,ZNF552,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,JDP2,RALGPS2,ARSK,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,SGPP1,PARP1,NCAPD2,TTBK2,ZBTB38,SLC4A8,ACTRT2,CYBRD1,NTAN1,FARS2,MFF,SPPL2B,ITGB4,FRMD4B,TMEM79,SLC37A1,ARMC9,PRDM2,CAT,OSBPL10,FBXW7,MERTK,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,NR1I2,RUNX1,UBASH3A,SNX4,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,TMEM64,CTSS,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,ZNF333,AAR2,PLA2G4A,HYAL2,ATG16L1,ICA1,MTA1,PADI6,CLTC,IFFO1,KIF13A,BBX,TNIP2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,HAL,LYN,CENPJ,SERBP1,GAS2L1,ACP6,VWA3B,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,ATXN7,PHF2,PEX14,PDE4C,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,GULP1,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CLCC1,A3GALT2,ZGPAT,NCOA2,ACTB,PIGC,TOP2B,MEIKIN,BAIAP2,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,ST3GAL5,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,PCNA,LETM1,LPIN2,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,NACC1,LITAF,MYO1F,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,DIXDC1,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,IL10RA,LRCH3,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,NDUFS6,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,SERPINF1,SLC25A10,TMEM168,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,MRPL55,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,GMPPB,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,FYCO1,C17orf63,MICU1,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,APLF,LIMCH1,GLYCTK,GNA15,CNKSR3,LOC81691,WIZ,ZDHHC14,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,B3GALNT1,NUDT19,GPRC5A,ALDH6A1,GALNT11,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,EDEM3,CARS,RAB8B,CHST3,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,GPS2,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,ALG14,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,AMPD2,AFTPH,ACIN1,TOR1B,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,ELP6,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,ST8SIA6,RCBTB2,COG2,RUNX2,NCLN,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,GCNT3,ZNF565,C1orf9,PRKAR2A,ZNF740,PCM1,RNASET2,MTMR7,ZNF518B,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,MARK4,NAGLU,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,KLHDC3,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1562                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ACOT7,SEC31B,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,PTAFR,GUSB,MSMP,GNB5,TMED3,EVL,AKAP1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,SLC25A26,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,ACOX1,ATG14,NENF,SMURF1,RNF220,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,HMBS,NDST2,PCSK6,NOLC1,MINK1,CLC,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,UQCC1,HORMAD2,MAP3K7CL,CCM2,EPHB2,CHP1,VPS53,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,SYNDIG1,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,HHAT,GALNT6,TBC1D5,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,HEXA,MTMR3,TFR2,SH3GL1,GGCX,NDOR1,PDCL,BCKDHA,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,SLC39A4,TPST1,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,RNF122,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,MLX,DAG1,KRT8,LGALS8,WIPI1,URI1,UBXN11,AMPD3,SWAP70,CEL,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,WWP2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,RALGDS,NUTF2,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,PDLIM7,APTX,SLC17A4,CS,UBAC2,NAPB,PTPRJ,CORO1C,MFSD2A,ASAP1,PICALM,GNAQ,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,MYLK,TMOD3,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,SLC23A2,PRX,RREB1,HCFC1R1,ERGIC1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,SLC12A4,PROZ,USP20,TAF4B,RPS6KA2,LRSAM1,CATSPER4,RNF40,AK8,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,PPP1R16B,NCK2,ST3GAL4,RNF157,IKZF1,HECW1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,BAIAP2L1,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,COL20A1,NEDD4L,RASSF2,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,SIK3,EML3,SNX9,MCMBP,DNAJC3,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,EVPL,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,ATG13,NEK8,PHTF2,LARP1,CACNA1D,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,OSBPL3,SEPT9,CAPN2,DENND2D,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,PIGL,NPL,GTPBP1,HPX,CLDN10,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,MAPRE3,LRRC8D,ASB8,ZDHHC18,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SND1,RCC2,PAFAH2,SLIT3,USP19,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,RALBP1,RIC8B,PHACTR1,COL4A1,WWOX,SEC14L2,NAPA,LEF1,OSBP2,HDC,PRNP,RHBDD2,C16orf70,IQCD,DHX30,THG1L,KRT72,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,HNMT,THADA,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,FCGR2A,ENO3,XPR1,RBPMS,ARSG,RASGRP1,ITGA2,OPA3,HNRNPM,SIPA1L3,RMND1,CTSZ,PTPN18,LGR5,INPP5F,IL1B,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,ABAT,ANO6,STOML1,POMGNT1,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,ALDH2,TOP1MT,DIDO1,ZNF175,LCP1,PARP9,CLSTN3,PHKB,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,EMC1,TAOK2,MCPH1,POC1A,LAX1,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ERP29,ADAM19,PCCA,TBL2,STT3A,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,CHST11,P4HTM,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,LFNG,LGALS12,GDPD5,MYO9B,DNAJC18,PPP2R5C,OPALIN,SLC35D1,RNF24,CD4,DNAH2,CEACAM1,TTC17,DNMT3A,MACF1,SRF,TMED10,LGR6,PDE9A,AACS,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,MTFR1,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,PRKAB1,KDELC2,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,GABARAPL1,MAPKAPK3,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ATG7,ACSF2,RHOH,SRC,PCBP2,SACS,C20orf203,MTHFD2,TBXAS1,CRTC3,PDE4D,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,PPP2R5E,TRIM16,MARK3,NACC2,CAMP,BBS1,RASSF5,ATXN1,CLTCL1,HDAC9,TMCC2,ARFGAP2,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,SLC25A45,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,STIM2,KIF26A,UPP2,ARHGEF7,SYTL3,BCL9,CHMP1A,FAIM2,VDR,RAD21,SPECC1L-ADORA2A,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,HIF1A,SAG,DOCK2,ILKAP,TNRC18,EIF4EBP1,RGS9,EEF2K,TRPM4,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,SLMAP,PTP4A2,CCDC136,AGPS,PQLC2,ST3GAL2,BICD1,LSM3,CDC42BPB,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,MTURN,LSM2,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,CFAP43,RFX2,PSMD6,IFI35,MAP3K14,SART1,SLC25A3,PLAGL1,AP1M1,SLC2A5,ITGB3,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,ARRDC2,ANXA9,WDR8,TMEM241,MED15,PRG3,CARD11,RYR1,GAPVD1,EPB41L2,GAPT,POLR1C,GNAI1,NR3C1,NAA25,SMIM22,SCOC,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,NT5E,UST,ZRANB1,OSBPL6,TRIM71,EFR3A,SRPK1,RBM14,NANS,ETV6,VPS52,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,FBXW11,MIEF2,LOXL1,OGDH,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SPPL3,EYA3,SDCCAG8,PLA2G6,BDKRB2,SNAP47,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,PEBP4,DYRK2,RXRB,APOL3,SPATA24,DMXL1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,PIGV,TMEM123,PHF1,HSD17B12,PMM1,PTPRC,AP2B1,ZC3H14,RANBP3,SPATA5,ARAP1,TUBD1,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,ADRBK2,ARID4A,PELI1,LIMD1,CHST15,SPIRE1,RAB7A,FMNL1,SPTBN2,ARHGAP10,HLCS,PEX2,FARP2,STX2,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,FYN,RBKS,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,RNF13,EPAS1,PER2,ASAP2,WWC2,ERMN,TMEM63A,TRIM29,PIK3CB,GNS,SPECC1,PPP2R5B,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,CEP128,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,COL4A3BP,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,ARFGEF2,MAP3K8,VEGFA,LRCH1,UQCRH,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,APP,GPSM1,SEC62,YARS,RASSF1,CSAD,SLC35C1,IGF2BP2,SENP7,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ACOXL,ZFYVE21,LAPTM4A,HBZ,FADS1,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,GDA,ZBTB16,SYK,MAPKAP1,TIMP2,RFFL,H6PD,AFF3,RIOK2,NTRK1,CDK2,CYSTM1,CHPT1,RPS6KA4,ECHDC1,GPR107,ANXA2,GTPBP2,EIF3M,GNB1,KRT71,FGF1,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,GGNBP2,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SDC1,DNAJB13,TLE1,PLA2G15,OLA1,GSAP,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,CPSF6,CREM,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,AMBRA1,SLC4A1,ERN1,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,PSMD13,TPPP3,FER,KLF7,FANCA,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,STUB1,RDH5,CDK19,CAPZA2,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,PTPRN2,TALDO1,MFSD10,DEDD,FOXO3,CAPN7,FUT4,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,BSCL2,FSCN3,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,NUP210,UCKL1,OTOF,TGFBRAP1,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,GMEB1,ZC3H4,MAPKAPK2,ORC1,RHOBTB3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,DPP9,CPNE2,MPV17,PALD1,CLCN6,NME2,VTI1B,MRAP,NPM3,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SLC7A6OS,SARM1,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,ECHDC3,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,GCNT2,KRT1,NET1,MAPRE2,NEK7,C10orf88,FARP1,STAMBPL1,AMFR,ACSF3,RAB25,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,RXRA,NOD1,TAOK3,ACADL,NME7,PARD3B,ZMYND10,ZDHHC1,PRKG2,CSNK1G3,FAM110B,TMEM117,DAPP1,ZNF438,EDEM2,XPC,GNA13,ALDH1A2,MYOM1,HNF4A,KANK1,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,TYSND1,MAFF,WEE1,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,KIF21B,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,ADCK1,GDPD3,RPL36AL,CAMTA1,PIGS,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,TP53BP1,ASPSCR1,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,CLPB,FAM168B,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,UPF3A,GET4,NFASC,GRK5,TBC1D14,RASAL2,COG7,TEX2,NDUFV2,CDH15,AGPAT3,SHB,HPS1,ATP8B2,STX17,CNPY3,XPNPEP3,SORBS2,PDZRN3,DCTN2,TPST2,BATF,GEMIN5,RDM1,MYO1A,SLC39A1,RHBDD1,FCRLB,FDFT1,PARP4,GLE1,GSTM4,NEK6,BRCA1,DEGS2,ITGB5,MNDA,SERPINB6,TTLL4,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,ACSM6,NRROS,STXBP2,OSBPL8,STAT5B,PNPLA2,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,SMG9,RGL1,LIG3,SORL1,TRPM2,RSU1,NFE2,DCTN5,MFSD12,TAF5L,LHFPL2,FNTB,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,PIEZO1,SAMD8,MT2A,CLEC16A,HIBADH,MX1,TRAK2,FURIN,UNK,WWP1,SLC25A13,UGT1A7,SNTB1,RAB7L1,FRYL,ARPC4,KRT31,RBM44,TEC,FANCC,SMAD5,ANXA4,SIRPA,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,PEX11A,INPP1,ACSL6,STARD10,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,TGFBR2,TULP4,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,NUSAP1,EHD4,LEPROTL1,ITPR2,EXOC4,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FAM174B,FBN1,RET,DUS2,RNF11,CHCHD6,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,ARHGAP35,ANP32B,TMEM130,ASL,SHANK2,THRSP,DLK1,ZBTB20,MKNK1,IRF7,MAT2B,HSPG2,PRIMPOL,BNIP3L,ATP6V1H,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,KIF13B,STK24,BET1L,ANKRD6,FLT3,WDR37,ZNF638,SLC30A1,RRBP1,GLUL,ANKS6,PIGR,PDE7A,TRAPPC12,SLC27A3,DHX8,SLC8B1,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,SLC38A10,TNFAIP1,CERKL,PPIC,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,CABLES1,SCAF8,DCLK3,UTRN,CSRP2BP,ATP2A2,STK11IP,FRY,MDN1,AKT2,ARMC4,PRDX3,MPL,DCP2,SIN3B,HRK,C6orf89,PARP10,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,TRIM2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,CLYBL,IVNS1ABP,RALGPS2,ARSK,SRSF7,RAB3IL1,SGPP1,PARP1,NCAPD2,TTBK2,SLC4A8,ACTRT2,CYBRD1,NTAN1,FARS2,MFF,SPPL2B,FRMD4B,TMEM79,SLC37A1,ARMC9,PRDM2,CAT,OSBPL10,FBXW7,MERTK,HNF1A,PSMD1,SCG3,CDC25C,MTSS1,UBASH3A,SNX4,CRLF3,ZC3H12C,SGIP1,STAT6,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,HS6ST1,NECAB1,EZR,AHI1,TMEM64,CTSS,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,PLA2G4A,HYAL2,ATG16L1,ICA1,MTA1,PADI6,CLTC,KIF13A,BBX,TNIP2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,HAL,LYN,CENPJ,SERBP1,GAS2L1,ACP6,VWA3B,AKT1,ACR,GRAMD4,UBTD2,UBXN1,UNC50,KPNA4,SLC1A3,ATXN7,PEX14,PDE4C,MAPK6,DOK4,MOSPD3,TFB1M,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,GULP1,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CLCC1,A3GALT2,NCOA2,ACTB,PIGC,TOP2B,BAIAP2,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,WT1,ST3GAL5,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,CLSTN1,PSMG1,ANKRD13B,LETM1,LPIN2,PHB2,PDLIM2,BUB3,NACC1,LITAF,MYO1F,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,SEC24A,DIXDC1,MDGA1,SFI1,LIPC,HCLS1,ERN2,MAP2K6,CREB3L1,FBXO9,IL10RA,LRCH3,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,NDUFS6,RABGAP1L,PKD2,USP1,NARS2,MSRA,ATL1,ZMIZ1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,C1GALT1,PPP2CB,PEX7,ARAP3,PLAA,IL15,ARNT,NEURL1B,SERPINF1,SLC25A10,TMEM168,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,MRPL55,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,GMPPB,ARID4B,PFKFB4,CEP295,ALOX5,COQ5,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,OAT,MGST2,FYCO1,MICU1,RBFOX2,DCTN4,PEAK1,FLOT1,CAND2,SPAG4,YOD1,NOX3,APLF,LIMCH1,GLYCTK,CNKSR3,ZDHHC14,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,B3GALNT1,NUDT19,GPRC5A,ALDH6A1,GALNT11,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,MAP3K4,NAPG,EDEM3,CARS,RAB8B,CHST3,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,PPP1CA,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,USP47,SPIRE2,SPTLC2,KLHL5,GPS2,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,RNF19A,CPT1A,SEMA4C,GSPT1,QKI,ARL2,ALG14,FKBP1B,MRPS14,BATF3,IQGAP1,AMPD2,AFTPH,ACIN1,TOR1B,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,BIK,NUCKS1,ELP6,PACS2,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ESYT2,SLC40A1,GALK2,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,ST8SIA6,RCBTB2,COG2,RUNX2,NCLN,PAK2,ALAS1,FLT1,CLCN7,DOCK10,EMID1,GCNT3,C1orf9,PRKAR2A,PCM1,RNASET2,MTMR7,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,MARK4,NAGLU,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,KLHDC3,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4
## [1] 5554    8
write.table(gem, file=file.path(res.dir, 
          paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hypo_", timeStamp, ".txt")),
           sep="\t", quote=F, row.names=F)

table(gem$Domain)
## 
## CORUM GO:BP GO:CC GO:MF    HP   HPA  KEGG MIRNA  REAC    WP 
##     1  1559   263   207  1169   409   167  1287   309   183
path.hypo <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hypo)
## [1] 659   8
#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hypo, filter = 'top')
# do the above steps again after restriction on effect size and genome-wide threshold of 5.8e-08
uniq.hyper <- merge_CG[merge_CG$Direction_camp_cra=="++",]
uniq.hypo <- merge_CG[merge_CG$Direction_camp_cra=="--",]

# Idea was that highest betas sometimes are at top but looks like that
# isn't the case here so I am not restricting by effect size for now
hyper.hist.cra <- ggplot(uniq.hyper) + geom_histogram(aes(beta_coeff_cra), bins=50) + labs(x="Hypermeth betas distribution CRA")
hyper.hist.camp <- ggplot(uniq.hyper) + geom_histogram(aes(logFC), bins=50) + labs(x="Hypermeth betas distribution CAMP")
hypo.hist.cra <- ggplot(uniq.hypo) + geom_histogram(aes(beta_coeff_cra), bins=50) + labs(x="Hypometh betas distribution CRA")
hypo.hist.camp <- ggplot(uniq.hypo) + geom_histogram(aes(logFC), bins=50) + labs(x="Hypometh betas distribution CAMP")
p <- grid.arrange(hyper.hist.cra,hyper.hist.camp,hypo.hist.cra, hypo.hist.camp, nrow = 2, ncol = 2)

ggsave(p, file=file.path(sub.plots.dir, 
                      "hist_hyper_hypo_cra_camp_betas.png"), width = 9, height = 9)

####################################
# Filter by genome-wide threshold
####################################
merge_CG_gw <- merge_CG[merge_CG$P.Value_cra<5.8e-08 & merge_CG$P.Value<5.8e-08,]
dim(merge_CG_gw)
## [1] 2865   62
uniq.hyper <- merge_CG_gw[merge_CG_gw$Direction_camp_cra=="++",]
uniq.hyper <- unique(uniq.hyper$Gene.x)
uniq.hyper <- uniq.hyper[uniq.hyper!="NA"]
uniq.hyper <- uniq.hyper[uniq.hyper!=""]
length(uniq.hyper) # 214
## [1] 214
uniq.hypo <- merge_CG_gw[merge_CG_gw$Direction_camp_cra=="--",]
uniq.hypo <- unique(uniq.hypo$Gene.x)
uniq.hypo <- uniq.hypo[uniq.hypo!="NA"]
uniq.hypo <- uniq.hypo[uniq.hypo!=""]
length(uniq.hypo) # 1,332
## [1] 1332
enrich.hyper <- gprofiler2::gost(query=uniq.hyper, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))
## Detected custom background input, domain scope is set to 'custom'
names(enrich.hyper)
## [1] "result" "meta"
# Results containing all annotated terms for hyper-methylated CpGs
gem <- enrich.hyper$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)
##            GO.ID                        Description term_size intersection_size
## 317   GO:0005737                          cytoplasm     11268               146
## 730 MIRNA:000000                         MIRNA root     14165               163
## 464  HPA:0530000                             spleen      5539                86
## 378   GO:0005488                            binding     15946               174
## 318   GO:0005622 intracellular anatomical structure     13844               158
## 465  HPA:0530711    spleen; cells in red pulp[≥Low]      5000                78
##     Domain          FDR Phenotype
## 317  GO:CC 1.278093e-09        +1
## 730  MIRNA 1.034643e-06        +1
## 464    HPA 1.412058e-06        +1
## 378  GO:MF 1.466783e-06        +1
## 318  GO:CC 1.893883e-06        +1
## 465    HPA 5.501473e-06        +1
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Genes
## 317                                                                                                                                                                         TFR2,ZMIZ1,TGFBR2,GSG1,RBKS,KIF5C,XYLT1,ABL1,RUFY4,CARS,ATN1,GALNT6,CELF2,COL23A1,UCK2,AZU1,VAV2,DAAM1,KIF13B,TARM1,ASB1,LPP,MGAT5,CAMKK2,POC1B,DTNB,TPP1,SERGEF,KIAA0319L,APP,GNG7,CAMK2G,NLRC4,CHST11,TERF2,PREX1,PRKAG2,MPO,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,SSH2,MOK,FAM193B,ZDHHC14,PPM1H,LRRK1,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,KLHL25,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,NEDD9,MKNK1,NISCH,CAMK1D,NGF,RBSN,EPB41L3,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,RHBDF2,CUX1,SPARC,KIAA0586,DYM,TNF,RPTOR,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,PPP2R5C,EFR3B,TNS3,GDI2,ARRDC5,MARCO,FCN1,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,FKBP15,SYNJ2,ABCA13,CCRL2,UBASH3B,TMEM150B,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,CREB3L4,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,LITAF,TNFRSF1B,KCNAB2,SDCCAG8,AP1G1
## 730                                                     ZMIZ1,TGFBR2,C20orf27,GSG1,KIF5C,TREM2,XYLT1,ABL1,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,UCK2,VAV2,DAAM1,KIF13B,ASB1,PCGF3,LPP,MGAT5,CAMKK2,KIAA1549L,DHX57,POC1B,DTNB,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,FBN2,CAMK2G,NLRC4,LYPD4,CHST11,TERF2,PREX1,MPO,SLX4IP,POLE,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,MACROD1,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,INTS6,SSH2,FAM193B,ZDHHC14,PPM1H,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GALNT14,CLEC5A,GLIPR2,OPRM1,NEDD9,MKNK1,CACNA2D2,NISCH,CAMK1D,RBSN,SSBP3,EPB41L3,CPM,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,CYB561D1,RHBDF2,CUX1,SPARC,KIAA0586,DYM,TNF,RPTOR,CCDC149,UBN1,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,GPX3,HLX,PPP2R5C,EFR3B,TNS3,GDI2,RBM20,FAM168A,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,PCOLCE2,FKBP15,SYNJ2,GATAD2A,ABCA13,CCRL2,UBASH3B,IL18RAP,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,TNFRSF1B,NAV3,VIT,SDCCAG8,AP1G1,NID1
## 464                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 TREM2,XYLT1,ABL1,CARS,ATN1,NCOR2,GALNT6,CELF2,AZU1,PCGF3,MGAT5,CAMKK2,TPP1,SERGEF,CHST11,TERF2,PREX1,TOR3A,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,INTS6,FAM193B,PPM1H,TTC7A,ZNF148,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GLIPR2,MKNK1,NISCH,PTX4,RBSN,PRDX5,TMEM8B,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,KIDINS220,CUX1,SPARC,DYM,TNF,RPTOR,TPD52L2,PCNT,FKBP9,DEFA4,PPP2R5C,GDI2,FCN1,AFAP1,TRIM27,JARID2,DYNC1H1,MYO18A,SIRPA,FKBP15,SYNJ2,GATAD2A,CCRL2,UBASH3B,IL18RAP,MIF4GD,TGOLN2,VTI1A,CREB3L4,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,KCNAB2,SDCCAG8,AP1G1
## 378 TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,UCK2,AZU1,VAV2,DAAM1,KIF13B,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,DHX57,POC1B,DTNB,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,FBN2,CAMK2G,NLRC4,TERF2,PREX1,PRKAG2,MPO,SLX4IP,POLE,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,MACROD1,WDFY1,SVIL,TNN,DENND2D,PRKCH,PSMB7,INTS6,SSH2,MOK,FAM193B,PPM1H,LRRK1,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,KLHL25,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,SLC10A1,NEDD9,MKNK1,CACNA2D2,NISCH,PTX4,CAMK1D,NGF,RBSN,SSBP3,EPB41L3,CPM,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,CYB561D1,RHBDF2,CUX1,SPARC,DYM,TNF,RPTOR,UBN1,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,GPX3,HLX,PPP2R5C,EFR3B,MIR145,TNS3,GDI2,RBM20,ARRDC5,MARCO,FAM168A,FCN1,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,PCOLCE2,FKBP15,SYNJ2,GATAD2A,ABCA13,CCRL2,UBASH3B,IL18RAP,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,CREB3L4,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,TNFRSF1B,KCNAB2,NAV3,VIT,SDCCAG8,AP1G1,NID1
## 318                                                                                                  TFR2,ZMIZ1,TGFBR2,GSG1,RBKS,KIF5C,XYLT1,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,UCK2,AZU1,VAV2,DAAM1,KIF13B,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,POC1B,DTNB,TPP1,SERGEF,KIAA0319L,APP,GNG7,CAMK2G,NLRC4,CHST11,TERF2,PREX1,PRKAG2,MPO,POLE,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,MACROD1,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,INTS6,SSH2,MOK,FAM193B,ZDHHC14,PPM1H,LRRK1,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,NEDD9,MKNK1,NISCH,CAMK1D,NGF,RBSN,SSBP3,EPB41L3,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,RHBDF2,CUX1,SPARC,KIAA0586,DYM,TNF,RPTOR,UBN1,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,HLX,PPP2R5C,EFR3B,TNS3,GDI2,RBM20,ARRDC5,MARCO,FCN1,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,FKBP15,SYNJ2,GATAD2A,ABCA13,CCRL2,UBASH3B,TMEM150B,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,CREB3L4,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,LITAF,TNFRSF1B,KCNAB2,NAV3,SDCCAG8,AP1G1
## 465                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    TREM2,XYLT1,ABL1,CARS,ATN1,NCOR2,GALNT6,CELF2,AZU1,PCGF3,MGAT5,CAMKK2,TPP1,CHST11,TERF2,PREX1,WDFY1,SVIL,DENND2D,PRKCH,GM2A,FAM193B,PPM1H,TTC7A,ZNF148,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GLIPR2,MKNK1,NISCH,PTX4,RBSN,PRDX5,TMEM8B,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,KIDINS220,CUX1,SPARC,DYM,TNF,RPTOR,TPD52L2,PCNT,FKBP9,DEFA4,PPP2R5C,GDI2,FCN1,AFAP1,JARID2,DYNC1H1,MYO18A,SIRPA,FKBP15,SYNJ2,GATAD2A,CCRL2,UBASH3B,IL18RAP,TGOLN2,CREB3L4,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,KCNAB2,SDCCAG8,AP1G1
## [1] 745   8
write.table(gem, file=file.path(res.dir, 
     paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hyper_gwthresh_", timeStamp, ".txt")),
     sep="\t", quote=F, row.names=F)

table(gem$Domain)
## 
## CORUM GO:BP GO:CC GO:MF    HP   HPA  KEGG MIRNA  REAC    WP 
##    96   220    61    41    45   258     8     4    11     1
path.hyper.gw <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hyper.gw)
## [1] 20  8
#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hyper.gw, filter = 'top')
enrich.hypo <- gprofiler2::gost(query=uniq.hypo, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))
## Detected custom background input, domain scope is set to 'custom'
# for results containing all annotated terms
gem <- enrich.hypo$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)
##             GO.ID                        Description term_size
## 2254 MIRNA:000000                         MIRNA root     14165
## 958    GO:0005737                          cytoplasm     11268
## 1124   GO:0003674                 molecular_function     17356
## 1125   GO:0005515                    protein binding     13924
## 1126   GO:0005488                            binding     15946
## 959    GO:0005622 intracellular anatomical structure     13844
##      intersection_size Domain          FDR Phenotype
## 2254              1042  MIRNA 1.267017e-66        +1
## 958                879  GO:CC 4.864073e-54        +1
## 1124              1144  GO:MF 7.088657e-54        +1
## 1125              1006  GO:MF 7.088657e-54        +1
## 1126              1091  GO:MF 8.698490e-54        +1
## 959               1001  GO:CC 1.614487e-53        +1
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Genes
## 2254                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,TTC7A,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,NHLRC4,KIAA1522,GNB5,TMED3,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,TNIK,TRIM9,DAPK2,TFF2,GFOD1,IL5RA,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,IL4,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,PNN,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CBFB,EPHB2,TTYH3,CHP1,VPS53,ZNF48,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,C6orf132,ERMAP,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,ITGAL,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,SH3GL1,NCOR2,ENTPD1,SLCO3A1,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,GALNT10,NVL,POR,AXIN1,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,CCDC127,HK2,DYRK1A,MLX,BATF2,DAG1,KRT8,LGALS8,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,PLXNA2,ANKRD52,SERINC5,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,BACH1,MAP6D1,C11orf24,DPH7,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,MAP1LC3B2,BDH1,FHL2,CMBL,TANGO2,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,SLC41A1,SSBP3,FOXJ3,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,AQP1,GPR156,DENND3,FCHSD2,CDH1,TMEM86B,FBXO7,ABCB9,CCDC85C,GRAMD1B,CALML4,PELI2,PHLDB3,SIAH2,MICAL2,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,SLC23A2,RREB1,PSTPIP2,TMEM154,ABCC4,ADAMTS14,PDE4B,GNG12,PI4KA,NADK,ZC3H11A,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,ZKSCAN5,RBL2,GSN,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,CAB39,GALM,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,NCK2,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,WNT3,GALNT7,UXS1,MTUS2,DHCR24,PHF13,C19orf54,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,CDKN2AIPNL,WDFY2,AGAP3,MAML1,EFNB2,ATG13,PHTF2,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,CHRNE,LRRC8C,P2RX7,PIK3AP1,LINC00548,P3H2,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,NBPF8,STON1-GTF2A1L,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,XAF1,ERG,NEDD4L,VAMP1,AGXT,NAP1L4,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,COL4A1,ARL15,SELPLG,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,B3GALNT2,THADA,ELL2,RAPGEF1,HDAC4,EXT1,ACTN4,GPD2,C16orf45,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,PTPN1,UNC5B,AAK1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,RALY,DIDO1,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,TMEM156,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,ARHGAP18,EIF4G2,PELP1,CHST11,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,MYO9B,MYLK4,ERI3,RNF24,CD4,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,LAX1,AACS,MICAL1,ACAD8,MRPS27,TRPV6,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ERAP2,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,RBM33,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,SERF2,UGGT1,EXD2,SMG5,EARS2,TESK2,ACSF2,SPNS3,SCAF11,SRC,PCBP2,SHBG,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,RASSF5,TMEM41A,HDAC9,SLC44A4,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,ART3,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TMEM220,AKR1E2,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,MAP3K14,BANK1,WDR70,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,HNRNPLL,WDR8,PRG3,HECTD4,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,EFR3A,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,BAZ1A,HSD17B12,PTPRC,AP2B1,C6orf47,ZC3H14,SPATA5,POLR1A,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,PEX2,IDO1,NAA16,PIWIL2,CELF2,FYN,ARPP19,ABTB2,MED13L,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,CEP128,BLVRA,SPRED2
## 958                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ACOT7,SEC31B,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,PTAFR,GUSB,MSMP,GNB5,TMED3,EVL,AKAP1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,SLC25A26,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,ACOX1,ATG14,NENF,SMURF1,RNF220,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,HMBS,NDST2,PCSK6,NOLC1,MINK1,CLC,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,UQCC1,HORMAD2,MAP3K7CL,CCM2,EPHB2,CHP1,VPS53,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,SYNDIG1,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,HHAT,GALNT6,TBC1D5,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,HEXA,MTMR3,TFR2,SH3GL1,GGCX,NDOR1,PDCL,BCKDHA,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,SLC39A4,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,RNF122,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,MLX,DAG1,KRT8,LGALS8,WIPI1,URI1,UBXN11,AMPD3,SWAP70,CEL,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,PDLIM7,APTX,SLC17A4,CS,UBAC2,NAPB,PTPRJ,CORO1C,MFSD2A,ASAP1,PICALM,GNAQ,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,TMOD3,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,SLC23A2,RREB1,PSTPIP2,HCFC1R1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,PROZ,USP20,TAF4B,RPS6KA2,LRSAM1,RNF40,AK8,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,NCK2,ST3GAL4,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,COL20A1,RASSF2,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,EML3,SNX9,MCMBP,DNAJC3,WNT3,GALNT7,UXS1,MTUS2,DHCR24,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,SERP2,WDFY2,TBC1D10A,AGAP3,ATG13,PHTF2,LARP1,CACNA1D,STK3,LRRC8C,P2RX7,PIK3AP1,P3H2,OSBPL3,SEPT9,CAPN2,DENND2D,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,RCC2,PAFAH2,SLIT3,USP19,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,RALBP1,RIC8B,PHACTR1,COL4A1,WWOX,NAPA,LEF1,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,DNAH1,B3GALNT2,HNMT,THADA,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,ENO3,XPR1,RBPMS,ARSG,RASGRP1,HNRNPM,SIPA1L3,RMND1,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ABAT,ANO6,PIK3R5,TMOD1,MAP2K5,UBE2D3,ALDH2,DIDO1,ZNF175,PARP9,CLSTN3,PHKB,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,KCNAB2,ARHGAP18,EIF4G2,PELP1,CHST11,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,SIL1,LSM14A,INSC,MYO9B,RNF24,CD4,DNAH2,TTC17,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,PIGL,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,TKT,PTEN,PRKAB1,KDELC2,ADD1,PLEKHA7,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SRC,PCBP2,C20orf203,MTHFD2,TBXAS1,CRTC3,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,NACC2,CAMP,RASSF5,CLTCL1,HDAC9,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,UPP2,ARHGEF7,SYTL3,FAIM2,RAD21,SPECC1L-ADORA2A,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,ILKAP,EEF2K,TRPM4,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,SLMAP,PTP4A2,AGPS,FMO1,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,WDFY4,USP7,IFI35,MAP3K14,AP1M1,SLC2A5,TRAPPC10,MTA3,GOLGA3,TINAGL1,WDR8,PRG3,GAPVD1,EPB41L2,GAPT,POLR1C,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,EFR3A,SRPK1,MTURN,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SPPL3,BDKRB2,SNAP47,CCDC47,RARG,PEBP4,DYRK2,RNF43,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,HSD17B12,PTPRC,AP2B1,ZC3H14,SPATA5,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,ADRBK2,ARID4A,LIMD1,CHST15,ARHGAP10,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,SPOP,STK10,EPAS1,WWC2,ERMN,TMEM63A,PIK3CB,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,TMEM201,DAZAP1,PGM1,CEP128,BLVRA,SPRED2
## 1124 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,SLC4A5,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,TTYH3,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,GNAO1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,CCL18,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,SSBP3,FOXJ3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,GPR156,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,ADTRP,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,RREB1,PSTPIP2,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,TNN,NCK2,ST3GAL4,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,KAT8,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,ELL3,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,EFNB2,ATG13,CD7,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,CHRNE,LRRC8C,P2RX7,PIK3AP1,P3H2,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,ST7,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,DNAH1,B3GALNT2,HNMT,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,C16orf45,ENO3,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,FTCDNL1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,UNC5B,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,PIK3R5,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,RALY,DIDO1,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,KCNAB2,ARHGAP18,EIF4G2,PELP1,CHST11,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,ATP1A4,MYO9B,MYLK4,ERI3,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,TRPV6,PIGL,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,RBM33,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SPNS3,SCAF11,SRC,PCBP2,SHBG,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,DLGAP1,RASSF5,TMEM41A,CLTCL1,HDAC9,SLC44A4,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,SLC14A2,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,ART3,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TMEM220,AKR1E2,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,IFI35,MAP3K14,BANK1,WDR70,MEGF10,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,CLCN1,PRG3,HECTD4,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,SRPK1,AGER,PLB1,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,SPATA5,POLR1A,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,CCL23,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,ECT2L,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,ABTB2,MED13L,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,OR2B2,DAZAP1,PGM1,BLVRA,SPRED2
## 1125                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,TESC,USP32,TRPC4AP,IGF1R,TRAPPC9,UVRAG,MUC13,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,MAP3K1,GNAO1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ABR,DOCK1,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,GLYR1,SLC18A2,DPPA3,SLC41A1,SSBP3,FOXJ3,CLRN1,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,FBXO7,ABCB9,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,ADTRP,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,ZNF789,PSTPIP2,TMEM154,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,KEL,CAB39,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,TNN,NCK2,IKZF1,GSTM3,TGFA,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,SOAT2,MAN1C1,RAP1GAP2,MED12L,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,KAT8,WNT3,UXS1,MTUS2,DHCR24,CDH23,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,TTLL6,NELFCD,TESPA1,TOPBP1,PACSIN2,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,EFNB2,ATG13,CD7,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,LRRC8C,P2RX7,PIK3AP1,P3H2,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,ST7,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,DGKI,NLRC5,RBX1,SGSM3,TGFB3,EIF6,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ATP2A3,AHNAK,DNAH1,B3GALNT2,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,C16orf45,ENO3,ZNF699,GDF5,RBPMS,RASGRP1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,UNC5B,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,RALY,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,EHBP1,CHCHD3,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,EIF4G2,PELP1,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,ATP1A4,MYO9B,MYLK4,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,MRPS27,TRPV6,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,UGGT1,EXD2,SMG5,SARNP,TESK2,ACSF2,SCAF11,SRC,PCBP2,SHBG,MTHFD2,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,DLGAP1,RASSF5,TMEM41A,CLTCL1,HDAC9,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,MYLK,HIPK2,SAG,SLC14A2,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,LHPP,MUC20,TMEM220,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,IFI35,MAP3K14,BANK1,WDR70,MEGF10,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,CLCN1,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,ZRANB1,OSBPL6,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,STAT4,TRAF1,F5,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,POLR1A,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,CCL23,LIMD1,CHST15,TCF7,ARHGAP10,ECT2L,PEX2,FARP2,NAA16,DOCK2,PIWIL2,FYN,RBKS,ARPP19,ABTB2,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,HERC1,ANKRD13A,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,BLVRA,SPRED2
## 1126                                                                                                                                                                                                                                                                                                                                                                                         ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,ABCC1,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,GNAO1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,SSBP3,FOXJ3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,ADTRP,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,RREB1,PSTPIP2,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,TNN,NCK2,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,METTL16,RAP1GAP2,MED12L,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,ZNF532,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,KAT8,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,EFNB2,ATG13,CD7,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,LRRC8C,P2RX7,PIK3AP1,P3H2,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,ST7,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,PAFAH2,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,DNAH1,B3GALNT2,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,C16orf45,ENO3,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,FTCDNL1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,UNC5B,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,PIK3R5,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,RALY,DIDO1,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,EIF4G2,PELP1,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,ATP1A4,MYO9B,MYLK4,ERI3,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,TRPV6,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,RBM33,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SCAF11,SRC,PCBP2,SHBG,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,DLGAP1,RASSF5,TMEM41A,CLTCL1,HDAC9,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,MYLK,HIPK2,SAG,SLC14A2,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TMEM220,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,IFI35,MAP3K14,BANK1,WDR70,MEGF10,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,CLCN1,PRG3,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,ZRANB1,OSBPL6,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,SPATA5,POLR1A,TUBD1,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,CCL23,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,ECT2L,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,ABTB2,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,BLVRA,SPRED2
## 959                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,GUSB,TCEA2,MSMP,GNB5,TMED3,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,MED25,ZBTB32,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,GNAO1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SSBP3,FOXJ3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,PICALM,GNAQ,MAFK,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,MICAL2,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,RREB1,PSTPIP2,HCFC1R1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,NCK2,ST3GAL4,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,TLDC2,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,ZNF532,EML3,SNX9,MCMBP,DNAJC3,KAT8,WNT3,GALNT7,UXS1,MTUS2,DHCR24,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,ATG13,PHTF2,LARP1,CACNA1D,STK3,LRRC8C,P2RX7,PIK3AP1,P3H2,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,MBD6,RCC2,PAFAH2,SLIT3,USP19,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,WWOX,NAPA,LEF1,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,DNAH1,B3GALNT2,HNMT,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,C16orf45,ENO3,XPR1,ZNF699,RBPMS,ARSG,RASGRP1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,IKZF2,PIK3R5,TMOD1,MAP2K5,UBE2D3,PHF12,ALDH2,RALY,DIDO1,ZNF175,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,KCNAB2,ARHGAP18,EIF4G2,PELP1,CHST11,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,MYO9B,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,PIGL,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SCAF11,SRC,PCBP2,C20orf203,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,RASSF5,CLTCL1,HDAC9,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,UPP2,ARHGEF7,SYTL3,FAIM2,RAD21,SPECC1L-ADORA2A,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,WDFY4,USP7,RPRD1A,SPIDR,IFI35,MAP3K14,WDR70,AP1M1,SLC2A5,TRAPPC10,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,PRG3,GAPVD1,EPB41L2,GAPT,POLR1C,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,EFR3A,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SPPL3,BDKRB2,SNAP47,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,ZC3H14,SPATA5,POLR1A,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,ADRBK2,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,MED13L,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,CEP128,BLVRA,SPRED2
## [1] 2669    8
write.table(gem, file=file.path(res.dir, 
      paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hypo_gwthresh_", timeStamp, ".txt")),
            sep="\t", quote=F, row.names=F)

table(gem$Domain)
## 
## CORUM GO:BP GO:CC GO:MF    HP   HPA  KEGG MIRNA  REAC    WP 
##     1   956   166   149   510   375    96   308    61    47
path.hypo.gw <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hypo.gw)
## [1] 204   8
#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hypo.gw, filter = 'top')

4. enrichment gprofiler2 including CRA, CAMP and FHS

# Now including FHS but not filtering by genome-wide threshold here as we already have a smaller percentage of overlap (n=193 CpGs)

uniq.hyper <- merge_CG.all[merge_CG.all$Direction_camp_cra_fhs=="+++",]
uniq.hyper <- unique(uniq.hyper$Gene.x)
uniq.hyper <- uniq.hyper[uniq.hyper!="NA"]
uniq.hyper <- uniq.hyper[uniq.hyper!=""]
length(uniq.hyper) # 5 genes only; will end up with nothing significant so not saving them
## [1] 5
#[1] "CBFA2T3" "ITGA5"   "B4GALT1" "FEZ2"    "APBB1"  
#write.table(uniq.hyper, file=file.path(res.dir, 
#              "cra_camp_fhs_uniq_hypermeth_genes.txt"),
#            sep="\t", quote=F, row.names=F)

uniq.hypo <- merge_CG.all[merge_CG.all$Direction_camp_cra_fhs=="---",]
uniq.hypo <- unique(uniq.hypo$Gene.x)
uniq.hypo <- uniq.hypo[uniq.hypo!="NA"]
uniq.hypo <- uniq.hypo[uniq.hypo!=""]
length(uniq.hypo) # 139 genes
## [1] 139
write.table(uniq.hypo, file=file.path(res.dir, 
              paste0("cra_camp_fhs_uniq_hypometh_genes_", timeStamp, ".txt")), 
              sep="\t", quote=F, row.names=F)

# gprofiler2 enrichment
enrich.hyper.all <- gprofiler2::gost(query=uniq.hyper, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))
## Detected custom background input, domain scope is set to 'custom'
names(enrich.hyper.all)
## [1] "result" "meta"
gem <- enrich.hyper.all$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]

# does not look very meaningful because of the gene/term size and the intersection size
head(gem); dim(gem)
##        GO.ID                Description term_size intersection_size Domain
## 1 CORUM:2385        ITGA5-ITGB4 complex         2                 1  CORUM
## 2 CORUM:2882 ITGA5-ITGB3-COL6A3 complex         3                 1  CORUM
## 3 CORUM:2384 ITGA5-ITGB1-ADAM15 complex         3                 1  CORUM
## 4  CORUM:143     APP-APBB1-LRP1 complex         3                 1  CORUM
## 5 CORUM:3112   ITGA5-ITGB1-SPP1 complex         3                 1  CORUM
## 6 CORUM:5870  APBB1-TSHZ3-HDAC1 complex         3                 1  CORUM
##            FDR Phenotype Genes
## 1 0.0009201427        +1 ITGA5
## 2 0.0009201427        +1 ITGA5
## 3 0.0009201427        +1 ITGA5
## 4 0.0009201427        +1 APBB1
## 5 0.0009201427        +1 ITGA5
## 6 0.0009201427        +1 APBB1
## [1] 89  8
write.table(gem, file=file.path(res.dir, 
     paste0("gProfiler2_cra_camp_fhs_logIgE_DMPs_enrich_hyper_", timeStamp, ".txt")),
        sep="\t", quote=F, row.names=F)

table(gem$Domain)
## 
## CORUM GO:CC GO:MF  KEGG  REAC    WP 
##    10    14    20    14    20    11
path.hyper.all <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hyper.all)
## [1] 45  8
#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hyper.all, filter = 'top')
enrich.hypo.all <- gprofiler2::gost(query=uniq.hypo, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))
## Detected custom background input, domain scope is set to 'custom'
# for results containing all annotated terms
gem <- enrich.hypo.all$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)
##            GO.ID                            Description term_size
## 915 MIRNA:000000                             MIRNA root     14165
## 393   GO:0003674                     molecular_function     17356
## 151   GO:0008150                     biological_process     16625
## 152   GO:0009987                       cellular process     15915
## 716  HPA:0040081 bone marrow; hematopoietic cells[≥Low]      6102
## 717  HPA:0040000                            bone marrow      6102
##     intersection_size Domain          FDR Phenotype
## 915               110  MIRNA 9.872529e-10        +1
## 393               117  GO:MF 1.854176e-07        +1
## 151               115  GO:BP 4.535958e-07        +1
## 152               113  GO:BP 4.535958e-07        +1
## 716                63    HPA 8.133531e-07        +1
## 717                63    HPA 8.133531e-07        +1
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Genes
## 915                                            NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,LRIG1,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,NDFIP2,DOCK1,MFHAS1,MND1,ENG,AJAP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,LTBP4,UBE3B,TFF1,PHLDB3,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,SLC45A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 393 NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,LRRC43,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,CPSF4L,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,LRIG1,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,GUCA2A,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,ACP5,NDFIP2,DOCK1,MFHAS1,MND1,PRG2,ENG,AJAP1,FBP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,PNPLA1,LTBP4,UBE3B,TFF1,PHLDB3,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,SLC45A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 151               NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,CPSF4L,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,LRIG1,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,GUCA2A,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,ACP5,NDFIP2,DOCK1,MFHAS1,MND1,PRG2,ENG,AJAP1,FBP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,PNPLA1,LTBP4,UBE3B,TFF1,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,SLC45A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 152                             NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,CPSF4L,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,GUCA2A,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,ACP5,NDFIP2,DOCK1,MFHAS1,MND1,PRG2,ENG,AJAP1,FBP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,PNPLA1,LTBP4,UBE3B,TFF1,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 716                                                                                                                                                                                                                                                                                                                                                              NDOR1,NCOR2,NDUFS6,ST3GAL1,LPCAT2,PCYT1A,B4GALT7,AXIN1,EZH2,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,LRIG1,MITF,PRKCZ,TTC7A,PRKCH,TNIK,MCM2,CAB39,AGPAT1,FBXW8,LPIN1,DOCK1,MND1,PRG2,BICD2,TOMM34,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,LMAN2,IGF1R,MECR,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,LTBP4,UBE3B,PHLDB3,SLC7A1,ELMO2,COL15A1,TRERF1,ATPAF2,INPP4A,KIAA1267,CTSB,RCC2,LBR,CLK3,GPR176,NFIA,BANK1,MICAL2,MPRIP
## 717                                                                                                                                                                                                                                                                                                                                                              NDOR1,NCOR2,NDUFS6,ST3GAL1,LPCAT2,PCYT1A,B4GALT7,AXIN1,EZH2,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,LRIG1,MITF,PRKCZ,TTC7A,PRKCH,TNIK,MCM2,CAB39,AGPAT1,FBXW8,LPIN1,DOCK1,MND1,PRG2,BICD2,TOMM34,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,LMAN2,IGF1R,MECR,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,LTBP4,UBE3B,PHLDB3,SLC7A1,ELMO2,COL15A1,TRERF1,ATPAF2,INPP4A,KIAA1267,CTSB,RCC2,LBR,CLK3,GPR176,NFIA,BANK1,MICAL2,MPRIP
## [1] 953   8
write.table(gem, file=file.path(res.dir, 
     paste0("gProfiler2_cra_camp_fhs_logIgE_DMPs_enrich_hypo_", timeStamp, ".txt")),
        sep="\t", quote=F, row.names=F)

table(gem$Domain)
## 
## CORUM GO:BP GO:CC GO:MF    HP   HPA  KEGG MIRNA  REAC    WP 
##   150   228    14    66   257   195     4    22    14     3
path.hypo.all <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hypo.all)
## [1] 21  8
#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hypo.all, filter = 'top')

5. clusterProfileR enrichment analysis for CRA and CAMP

bck.univ.plt <- mapIds(org.Hs.eg.db, uniq.ge.plt, 'ENTREZID', 'SYMBOL')
## 'select()' returned 1:many mapping between keys and columns
length(unique(bck.univ.plt))
## [1] 22656
bck.univ.plt.df <- data.frame(bck.univ.plt)
#bck.univ.plt.df <- bck.univ.plt.df[!is.na(bck.univ.plt.df$bck.univ.plt), ]
bck.univ.plt.df <- bck.univ.plt.df$bck.univ.plt
univ <- as.numeric(bck.univ.plt.df)
univ <- univ[!is.na(univ)]
univ <- as.character(univ)
#ids <- as.numeric(symbols.entrez)
#names(geneList) <- ids

coeff.cra <- merge_CG_gw$beta_coeff_cra
names(coeff.cra) <- merge_CG_gw$Gene.x
coeff.cra.df <- data.frame(coeff.cra)
coeff.cra.df$Gene <- names(coeff.cra)
coeff.cra.uniq <- coeff.cra.df$Gene[!is.na(coeff.cra.df$Gene)]
coeff.cra.uniq <- coeff.cra.df[!is.na(coeff.cra.df$Gene), ]
coeff.cra.uniq <- coeff.cra.df[coeff.cra.df$Gene!="NA",]
coeff.cra.uniq <- coeff.cra.df[!duplicated(coeff.cra.df$Gene), ]

coeff.cra.uniq.v <- coeff.cra.uniq$coeff.cra
names(coeff.cra.uniq.v) <- coeff.cra.uniq$Gene
geneList <- coeff.cra.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')
## 'select()' returned 1:1 mapping between keys and columns
length(symbols.entrez)
## [1] 1509
#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez))
## [1] 1390
ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)

edo.dgn <- enrichDGN(gene, pvalueCutoff = 0.05,pAdjustMethod = "BH",qvalueCutoff = 0.05)
barplot(edo.dgn, showCategory=20)

edo.dgn.ge <- setReadable(edo.dgn, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(edo.dgn.ge, categorySize="qvalue", foldChange=geneList)
## Warning: ggrepel: 96 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# without fold change
cnetplot(edo.dgn.ge, node_label="all", categorySize="qvalue")
## Warning: ggrepel: 77 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

enrichplot::dotplot(edo.dgn.ge, showCategory=30) + ggtitle("dotplot for DO")
## wrong orderBy parameter; set to default `orderBy = "x"`

pdf(file = file.path(sub.plots.dir, "dotplot_enrichDGN_CRA_CAMP.pdf"),width = 7, height = 7)
enrichplot::dotplot(edo.dgn.ge, showCategory=20) + ggtitle("dotplot for DO")
## wrong orderBy parameter; set to default `orderBy = "x"`
dev.off()
## png 
##   2
DT::datatable(edo.dgn.ge@result, filter = 'top')
## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html
# no gene sets enriched here for diseases using DysGeNET
gse.dgn <- gseDGN(geneList,
              minGSSize     = 10,
              maxGSSize = 500,
              pvalueCutoff  = 0.05,
              pAdjustMethod = "BH",
              verbose       = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## no term enriched under specific pvalueCutoff...
#dgn <- setReadable(dgn, 'org.Hs.eg.db')
#head(dgn, 3)
#enrichplot::dotplot(gse.dgn, showCategory=30) + ggtitle("dotplot for DO")

# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
x <- pairwise_termsim(edo.dgn.ge)
emapplot(x)

pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_gseDGN_CRA_CAMP_overlap_gw_genes.pdf"),
    width = 11, height = 9)
emapplot(x)
dev.off()
## png 
##   2
# nothing
enr.do <- enrichDO(gene = gene,
              ont           = "DO",
              pvalueCutoff  = 0.05,
              pAdjustMethod = "BH",
              universe      = univ,
              minGSSize     = 10,
              maxGSSize     = 500,
              qvalueCutoff  = 0.05,
              readable      = FALSE)
dim(enr.do) # nothing
## [1] 0 9
head(enr.do)
## [1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust   
## [7] qvalue      geneID      Count      
## <0 rows> (or 0-length row.names)
gene.df <- bitr(gene, fromType = "ENTREZID",
                 toType = c("ENSEMBL", "SYMBOL"),
                 OrgDb = org.Hs.eg.db)
## 'select()' returned 1:many mapping between keys and columns
## Warning in bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), :
## 1.37% of input gene IDs are fail to map...
head(gene.df)
##   ENTREZID         ENSEMBL  SYMBOL
## 1     3508 ENSG00000132740 IGHMBP2
## 2     4507 ENSG00000099810    MTAP
## 3    57705 ENSG00000128815   WDFY4
## 4    83445 ENSG00000111305    GSG1
## 6    90957 ENSG00000163214   DHX57
## 7    23136 ENSG00000082397 EPB41L3
# just returns functional profile of a geneset at a specific GO level not a P-value
ggo <- groupGO(gene     = gene,
                OrgDb    = org.Hs.eg.db,
                ont      = "BP",
                level    = 2,
                readable = TRUE)
dim(ggo)
## [1] 31  5
head(ggo)
##                    ID            Description Count GeneRatio
## GO:0000003 GO:0000003           reproduction    92   92/1390
## GO:0002376 GO:0002376  immune system process   295  295/1390
## GO:0006791 GO:0006791     sulfur utilization     0    0/1390
## GO:0006794 GO:0006794 phosphorus utilization     0    0/1390
## GO:0007610 GO:0007610               behavior    45   45/1390
## GO:0008152 GO:0008152      metabolic process   892  892/1390
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0000003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ZMIZ1/TGFBR2/ROPN1L/ADAM19/ZNF148/TRIM27/ASB1/CYP19A1/VDR/OPRM1/APP/ETV6/CREB3L4/PARK7/STAT3/DHX37/ELL3/RAD21/THRA/STAR/STK3/PTEN/IL1B/IFT27/EPAS1/TESK2/SLC6A4/DNAH1/SGPL1/DHCR24/SRPK1/GOLGA3/CALR3/LGR5/ACOX1/NCOR2/FBXW8/DAZAP1/ABHD2/RARG/NR2C2/SLIT3/ADA/SPATA5/PPP1R1B/ASH1L/PLB1/TAF4B/TCF7/SMARCC1/PIWIL2/SRC/TXNDC8/TGFB3/POC1A/IDO1/CAPN2/CD9/ARID4A/ACRBP/KLF1/GJB3/KRT8/SLC2A8/CEBPB/NUDT1/SLC19A1/WNT3/SIRT2/ADGRG1/BSG/CSDE1/ANGPT2/SAFB2/ABAT/FZR1/SPHK2/NOTCH2/GRB2/ARID1A/ATP1A4/HDAC4/HORMAD2/PTK2B/LIMK2/QRICH2/PTAFR/MND1/LEF1/CTSB/GCM1/PRKDC
## GO:0002376                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ABL1/ZMIZ1/TGFBR2/GM2A/DEFA4/VAV2/SLPI/TARM1/MARCO/CLEC5A/TRIM27/MPO/SLC7A7/GDI2/CYP19A1/SIRPA/UBASH3B/AZU1/AP1G1/OPRM1/TNFRSF1B/DYNC1H1/TNF/KIF13B/APP/NLRC4/ABCA13/ETV6/MIR145/CCRL2/HLX/GPR68/MYO18A/PSMB7/LRRK1/TREM2/FCN1/JARID2/IL18RAP/LTF/IL20/SIPA1L3/PARK7/STAT1/DOCK2/IL16/SRPK2/STAT3/IL10RB/PRG3/IFI35/HK1/SERPINC1/THRA/STAR/GAPT/DNAJC3/STK3/TRAF3/IL1B/RNF41/ITCH/BANK1/MECOM/PSMA2/EPAS1/MFSD6/SLC7A11/NOTCH4/EIF6/SH3RF1/TRIM8/ASH2L/SWAP70/HDAC9/KMT2C/PDE4B/SGPL1/CAPZB/RAB3B/LRRC8A/ATP11A/SRPK1/IL34/RASSF2/AMPD3/LAIR1/TMOD3/GLB1/SOCS6/RAB31/TAPBP/AGBL4/CCL23/NLRC5/GSN/CD4/IP6K2/FARP2/GPI/GTPBP1/ANO6/CREG1/CAMK1D/RARG/RNASE7/TRIB1/ADD1/ADAR/PTPN1/P4HTM/FKBP1A/PRKCB/IL1RL1/LRRC17/AGER/ADA/PIP4K2A/LSM14A/ZNF175/CD63/DLG5/CD81/PIK3R6/ERAP2/PRNP/PLAUR/CAB39/ORAI1/ALOX15/CD151/HDAC1/CLU/JAG1/TCF7/MSMP/ADAM8/NFAM1/XAF1/STK10/ADTRP/IFI27/CAP1/NCK2/CBFB/SSBP3/WNK1/SPI1/PILRB/ADARB1/SRC/IL13/LCP1/NDRG1/TGFB3/IDO1/CD9/ARID4A/SELPLG/PIK3CB/IL18BP/SETD1A/RSAD2/PRKCE/PREX1/KLF1/MTURN/NCF4/TMEM63A/PSMC1/RAPGEF1/CDK6/RAB20/CEBPE/UBR4/ABCB9/CREBBP/DOCK1/CD28/CRISPLD2/MYL9/CEBPB/CLEC4C/FAXDC2/SDC3/SLC2A5/LAX1/AP1M1/CLC/CALM1/HK3/HCK/GYG1/CAMK2G/PLA2G1B/MITF/SLC7A6/SH3PXD2A/CTNNBL1/SIRT2/FOXP1/ACTN1/IL4/CRTC3/SERINC5/RB1/MUC13/SEMA3C/BSG/LBR/TRPM4/ABR/KAT8/BATF2/AP2B1/CD59/PARP9/P2RX7/DSC1/CAMP/CDK5RAP3/KCNAB2/ELMO2/DGAT1/FADD/ANGPT2/OSBPL1A/CD7/USP15/PIK3R1/ITPKB/MCEMP1/PLD3/KLHL6/FBXO7/TESC/NFATC2/PICALM/ELMO1/SPPL3/EPX/TESPA1/SLC7A1/CCL18/PRKCZ/SPHK2/IL5RA/NOTCH2/BCL6B/PTPRC/PRG2/GRB2/MCU/SEMA4D/CLNK/MUC20/ITGAL/POLR3E/IGF1R/HDAC4/PTK2B/ARSB/COTL1/MFHAS1/TRIM26/PCBP2/PTPRJ/TTC7A/VPS33A/POLM/RAB5C/DAPK1/PTAFR/DOCK8/GUSB/IKZF1/FYN/CMTM6/LEF1/EFNB2/EVL/ERMAP/HIPK2/RASGRP1/PGM1/PRKCH/MAP3K1/CTSB/RAB37/TRIM4/PRKDC/DAPK2/MAP3K14/MAD1L1/ZFPM1
## GO:0006791                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## GO:0006794                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
## GO:0007610                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           GM2A/NGF/OPRM1/APP/PARK7/MFSD2A/STAT3/THRA/STAR/KCNA2/PTEN/EPHB2/SLC7A11/SLC6A4/INPP5F/PAK6/FBXL20/EPHA4/ASIC1/AGER/ADA/PPP1R1B/PRNP/DAB1/ADARB1/APBA2/IDO1/CAPN2/PRKCE/CEBPB/CDH23/TMOD1/FADD/MUSK/DGKI/HTT/PICALM/ABAT/PRKCZ/GNAO1/HDAC4/SLC18A2/FYN/HIPK2/GPR176
## GO:0008152 IGHMBP2/MTAP/WDFY4/ABL1/NEDD9/ZMIZ1/TGFBR2/XYLT1/GM2A/RBKS/CUX1/PCOLCE2/KIDINS220/VAV2/TERF2/SLPI/ROPN1L/ADAM19/CAMKK2/SMYD4/NAV3/LIPC/MARCO/TPP1/CLEC5A/ZNF148/TRIM27/ADGB/NGF/MIF4GD/MPO/PPM1H/MGAT5/UCK2/TUT1/SLC7A7/ASB1/GLIPR2/ADCY9/SSH2/ZDHHC14/SYNJ2/CYP19A1/TGOLN2/SIRPA/TFR2/FKBP9/ATN1/ACOXL/RHBDF2/ME3/CELF2/TMEM150B/UBASH3B/VDR/HIPK3/AZU1/ACACA/OPRM1/TNFRSF1B/DYNC1H1/TNF/MKNK1/TGFBI/POLE/PIK3C2B/RBM20/MACROD1/TRIM67/APP/NLRC4/CHST11/ZNF438/MOK/PPP2R5C/ETV6/MIR145/RUFY4/GPX3/HLX/LITAF/FKBP15/EFR3B/PRDX5/MYO18A/INTS6/PSMB7/LRRFIP1/KLHL25/IRAK2/LRRK1/CYB561D1/CRYL1/PCK2/TREM2/FCN1/JARID2/IL18RAP/PCGF3/LTF/CPM/ARRDC5/CREB3L4/FAM168A/SUFU/HSD17B12/FBXL2/ZBTB34/RALB/SECISBP2/F5/TECR/ZC3H14/ANKRD13A/RNF157/AKR1E2/ATP2A3/ART3/IL20/ERP29/ODC1/HECTD4/ITPKC/PARK7/STAT1/EXT1/MFSD2A/EEFSEC/IL16/COL15A1/ZNF699/SRPK2/STAT3/USP7/ACAD8/PITPNM2/DHX37/ELL2/RFT1/WIPI1/CCM2/STT3A/RALY/UCP3/MYLK4/ZKSCAN5/ACO1/WWOX/UBXN11/RNF10/PHACTR1/PRG3/CHCHD3/ZNRF1/FARSA/SPIDR/ELL3/RAD21/HK1/HECTD1/BAZ1A/KL/SERPINC1/SMYD3/BACH1/THRA/YEATS2/ATG13/DPPA3/MGAT4B/THG1L/STAR/KEL/P3H2/TOPBP1/DNAJC3/HIRA/ERI3/PDE9A/SLC2A9/BICD1/STK3/MIB1/TRAF3/PTEN/IL1B/TNXB/GSTO2/CBFA2T2/ARL6IP4/RNF41/ITCH/HNRNPM/BANK1/AGAP3/BRD4/ZDHHC3/EPHB2/MECOM/PSMA2/GLYR1/CDC42BPB/SAMD4B/NT5DC3/VPS39/ZNF609/LARP1/FOXJ3/VGLL4/CAMKMT/PPP2R5E/LHPP/WDFY2/EPAS1/TESK2/KLHL24/MTHFD2/ST3GAL2/PI4KA/AHCYL2/BLVRA/AK2/ZNF789/METTL17/SLC7A11/NOTCH4/CREB3L2/EIF6/LSM14B/SH3RF1/TRIM8/FBXL13/SLC6A4/BCKDHA/ASH2L/ANGEL1/TGFA/OBSL1/AACS/SWAP70/HDAC9/AKAP12/ZC3H11A/KMT2C/PDE4B/WWC2/GALM/CRABP2/TRERF1/HMGCL/CSNK1D/HPD/ACSM1/HERC1/GEMIN4/ZDHHC18/SUDS3/UBE2D3/SGPL1/OGDH/RMND1/GDF5/REV1/RNF103/PIP5K1B/POR/NR3C1/NXF1/SCPEP1/RAB3B/WDR70/CHAC1/DHCR24/EARS2/SLC45A3/OPA1/INPP5F/GALNT16/SREBF2/ZXDC/SRPK1/IL34/AGPS/RASSF2/AMPD3/LGALS8/DESI1/MED12L/GLB1/NEK3/ZBTB42/GNAQ/PELP1/SOCS6/RAB31/TAPBP/TCEA2/BCAT1/ACOX1/FOXK1/AGBL4/ALOX5AP/MAFK/RPTOR/CCL23/NLRC5/PAM16/NCOR2/AGPAT1/GSN/CD4/SIAH2/IP6K2/PHF20/EXD2/PAK6/MICAL1/TRAF1/GPI/FBXL20/GTPBP1/RHBDD2/FBXW8/DAZAP1/MTA3/FECH/ABHD2/CREG1/APTX/CAMK1D/MTFR1L/RARG/BDKRB2/EFNA3/SAP30L/PHF12/RNASE7/ACSF2/TRIB1/PNN/CS/ADD1/ADAR/EPS15/MAP6D1/PTPN1/TXNRD2/NPL/P4HTM/ASB8/AAK1/NR2C2/GALC/FKBP1A/SERPINB2/PRKCB/CHST15/USP32/EPHA4/URI1/ZNF628/UST/NELFCD/NDST2/NACC2/IL1RL1/PDE6H/DHX15/CORO1C/AGER/UGT1A8/SLIT3/ADA/PIP4K2A/LSM14A/MICAL2/ZNF175/DEPDC5/PPP1R1B/CD63/EHF/ASH1L/NVL/SAG/SECISBP2L/RPRD1A/PLB1/VTI1A/EP400/KANSL1/MCPH1/POLR1C/CTIF/RNASEH2C/FBXO32/ERC1/SERP2/CD81/PIGN/SARNP/RBL2/PIK3R6/ERAP2/PRNP/SULF2/ITSN1/PELI2/PLAUR/TTLL6/HNRNPLL/TFF1/GGCX/DIDO1/IFRD1/CAB39/ALOX15/ARNT2/ENO3/TAF4B/HDAC1/CLU/AGXT/MED13L/JAG1/TCF7/GALNT7/ZHX2/ERG/MED25/PI4KB/UBAC2/ACTN4/DYRK1A/MAP2K5/ADAM8/RYBP/NENF/CSGALNACT1/NFAM1/HMBS/ZEB2/HEXA/SCOC/NOLC1/INPP5A/SPOP/BCL7A/STK10/ADTRP/TMEM86B/DAB1/CHP1/DENND3/RNF220/GPD2/COPS3/MTCL1/IFI27/LDLRAD4/NCK2/CBFB/SSBP3/CMBL/TPCN2/ATG14/TRPC4AP/COASY/WNK1/SMARCC1/MVB12A/DCP1B/SPI1/SLC24A3/USP19/PIWIL2/YWHAQ/GALNTL6/PEX2/PILRB/ADAMTS14/GSTM3/MAN1C1/DNAJC6/ADARB1/SRC/IL13/CLK3/TXNDC8/PHKB/TGFB3/APBA2/LAMB1/ST6GALNAC4/JOSD1/PCSK6/ADORA3/MAPRE3/MCM2/MTMR10/IBTK/SSH1/TFDP2/SLC2A6/MAPK13/ACSL1/IDO1/MDM4/LTBP4/CHCHD10/PC/SLC17A4/CAPN2/CD9/ST3GAL1/ARSG/ARID4A/PIK3CB/SETD1A/RSAD2/PRKCE/SLC29A1/PCCA/PREX1/MLX/RNF24/PIGL/KLF1/RNF34/PFKFB3/MTURN/TET3/TPCN1/ZNF70/NCF4/SMURF1/MAML1/MRPS27/UVRAG/MAP4K4/PSMC1/RAPGEF1/ANAPC11/UGGT1/CDK6/AHNAK/MLST8/RBPMS/MTA2/ABCC1/PTPRE/DIS3L2/CEBPE/VPS13D/UXS1/UBR4/ZRANB1/CREBBP/NEMF/DAG1/ZNF662/PTDSS1/KLHL21/CD28/ARID3A/GPATCH1/KDM4B/CHD9/TADA2B/METTL16/ARPP19/PRKAB1/FOXJ2/RASSF5/RAB19/SLCO3A1/SLC2A8/ETFB/USP20/MIR1207/CEBPB/LRRC41/LIN52/XXYLT1/MYLK/FAXDC2/SDC3/CEL/SLC2A5/TNIK/FMO1/ARID1B/NUDT1/TRIM9/LAX1/ITPK1/RD3/FAM20B/NISCH/CLC/AKAP13/SLC19A1/LDB2/CDYL2/STAT4/CALM1/NEDD4L/HK3/GFPT2/RFC3/MBD6/SMG5/TLE4/HCK/NAA16/GYG1/CMTR1/RAP2A/CAMK2G/FHL2/ACVRL1/PLA2G1B/MGAT3/RNF144B/PRKAG2/GATAD2A/MITF/INTS9/SH3PXD2A/WNT3/EXD3/CTNNBL1/SGSM3/SIRT2/DAP/MCMBP/WWP2/CNOT8/LIMD1/FOXP1/RNF122/RPS6KA2/DYRK2/NADK/RNF40/ACTN1/IL4/CRTC3/SERINC5/RB1/ACCS/MUC13/UQCC1/ADGRG1/PAFAH2/BSG/RNF214/GALNT6/CSDE1/SUPT3H/LBR/MAX/NFIA/TRPM4/KAT8/BATF2/MECR/MINK1/MAP1LC3B2/SOAT2/GALNT10/AP2B1/MED27/PARP9/HNMT/P2RX7/TTC7B/NDUFV1/CDK5RAP3/KCNAB2/DPH7/UPP2/POLR1A/ITIH1/SLC7A14/DGAT1/FADD/MUSK/THADA/ANGPT2/WDR81/TKT/OSBPL1A/RBX1/TBXAS1/PNPLA1/DGKI/MEF2D/FADS2/HTT/ZBTB32/USP15/AK8/PIK3R1/NDOR1/MIR548AZ/ITPKB/DGKG/PDLIM1/CCDC47/TLE3/TRAP1/SAFB2/NCOA7/PLD3/KPNA1/EFR3A/TBC1D5/SEC16B/ZBTB22/CPSF4L/PRMT3/SASH1/FBXO7/GALNT12/COLQ/TESC/NFATC2/AFF1/PICALM/GRB10/CCNY/TGFB1I1/SPPL3/SGMS1/OSBPL3/EPX/GGA2/PIK3R5/RERE/ABCC4/ABAT/ENTPD1/CCL18/DMAP1/RECQL5/PTPN18/SLC25A33/FZR1/PRKCZ/SPHK2/NGFR/PTPRS/MLXIP/IL5RA/ALDH2/GALNT14/PNLIPRP3/NOTCH2/AXIN1/RFC2/ASCC1/BCL6B/UBE2O/SPTBN1/MAN2A2/PTPRC/RREB1/TMED10/GRB2/PXN/NR0B2/TRIM33/SNRNP200/ST3GAL4/SPRED2/TBC1D10A/SLC44A4/VKORC1L1/SEMA4D/ILKAP/CDCA7L/ASNSD1/CLNK/ARID1A/CARS2/MUC20/PAXBP1/DDC/EIF1AD/PCYT1A/POLR3E/IGF1R/HDAC4/BDH1/WDR20/MGLL/EIF4G2/LPIN1/IKZF2/AQP1/PTK2B/ARSB/DICER1/RNF43/GUCA2A/RCAN3/GRK4/MFHAS1/UBE4A/TRIM26/LIMK2/HHAT/INPP4A/PCBP2/EEF2K/UBE3B/PTPRJ/SLC18A2/TTC7A/QRICH2/ZNF48/GPHN/PROZ/VPS33A/GFOD1/NDFIP2/LTBP1/MTMR3/SLC25A25/FBP1/POLM/ZNF653/DAPK1/LPCAT3/OXNAD1/PTAFR/B3GALNT2/MGAT4A/GUSB/LRSAM1/IKZF1/FYN/MND1/SOGA1/SCAF11/SLC4A5/TRAPPC9/PTP4A2/HECW2/MYLK3/AREL1/ENG/LPCAT2/CDH1/OSBPL6/LEF1/ITPR1/EFNB2/USPL1/ACP5/ERMAP/HIPK2/RASGRP1/PGM1/PRKCH/TNFAIP8/MAP3K1/CTSB/MIPEP/HK2/EZH2/TRIM4/CACUL1/SAMD11/GCM1/CABIN1/GABARAPL1/ZBTB48/CDK17/PRKDC/NHLRC4/EIF3J/OSBPL5/MIR202/SNX9/DAPK2/SLC23A2/MAP3K14/KSR1/ZNF862/ACOT7/ZFPM1
ego <- enrichGO(gene          = gene,
                OrgDb         = org.Hs.eg.db,
                ont           = "BP",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.05,
                qvalueCutoff  = 0.05,
                readable      = TRUE)
dim(ego) # 251
## [1] 251   9
save(ego, file=file.path(res.dir,
                  paste0("enrich_GO_CRA_CAMP_gwthreshV1_", timeStamp, ".RData")))

write.table(ego@result,file=file.path(res.dir, 
       paste0("enrichGO_CRA_CAMP_gwthreshV1_",timeStamp,".txt"))
                ,sep="\t",row.names=F,quote=F)

head(ego)
##                    ID                                       Description
## GO:0030099 GO:0030099                      myeloid cell differentiation
## GO:0045637 GO:0045637        regulation of myeloid cell differentiation
## GO:1903706 GO:1903706                         regulation of hemopoiesis
## GO:1902105 GO:1902105           regulation of leukocyte differentiation
## GO:0043312 GO:0043312                          neutrophil degranulation
## GO:0002283 GO:0002283 neutrophil activation involved in immune response
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0030099   71/1233 431/18866 4.110661e-13 2.338144e-09 1.981339e-09
## GO:0045637   45/1233 263/18866 2.506735e-09 7.129156e-06 6.041233e-06
## GO:1903706   68/1233 498/18866 5.649299e-09 9.610415e-06 8.143847e-06
## GO:1902105   47/1233 290/18866 6.758379e-09 9.610415e-06 8.143847e-06
## GO:0043312   64/1233 487/18866 6.862848e-08 7.807176e-05 6.615786e-05
## GO:0002283   64/1233 490/18866 8.630413e-08 8.181632e-05 6.933099e-05
##                                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0030099 TGFBR2/CLEC5A/UBASH3B/TNF/APP/MIR145/GPR68/LRRK1/TREM2/LTF/IL20/STAT1/STAT3/THRA/RNF41/EPAS1/EIF6/ASH2L/KMT2C/IL34/RASSF2/TMOD3/CD4/FARP2/RARG/TRIB1/ADD1/ADAR/P4HTM/PRKCB/LRRC17/PIP4K2A/CD81/HDAC1/JAG1/CBFB/SPI1/SRC/ARID4A/SETD1A/KLF1/MTURN/CDK6/CEBPE/CREBBP/MYL9/CEBPB/FAXDC2/MITF/SH3PXD2A/FOXP1/ACTN1/IL4/RB1/LBR/KAT8/BATF2/CDK5RAP3/FADD/PIK3R1/ITPKB/TESC/NOTCH2/PTK2B/MFHAS1/VPS33A/IKZF1/LEF1/HIPK2/PRKDC/ZFPM1
## GO:0045637                                                                                                                                                              UBASH3B/TNF/MIR145/GPR68/TREM2/LTF/IL20/STAT1/STAT3/RNF41/EIF6/ASH2L/KMT2C/IL34/RASSF2/CD4/RARG/TRIB1/P4HTM/PRKCB/LRRC17/HDAC1/JAG1/CBFB/SPI1/SETD1A/MTURN/CDK6/CREBBP/MYL9/CEBPB/FAXDC2/MITF/FOXP1/IL4/RB1/FADD/PIK3R1/ITPKB/TESC/NOTCH2/PTK2B/LEF1/PRKDC/ZFPM1
## GO:1903706                       ABL1/ZMIZ1/TGFBR2/UBASH3B/TNF/MIR145/HLX/GPR68/PSMB7/TREM2/LTF/IL20/STAT1/STAT3/IL1B/RNF41/ITCH/PSMA2/EIF6/SH3RF1/ASH2L/KMT2C/IL34/RASSF2/CD4/RARG/TRIB1/P4HTM/PRKCB/LRRC17/AGER/ADA/PIK3R6/HDAC1/JAG1/TCF7/ADAM8/NFAM1/CBFB/SPI1/SETD1A/MTURN/PSMC1/CDK6/CREBBP/CD28/MYL9/CEBPB/FAXDC2/MITF/FOXP1/IL4/RB1/FADD/PIK3R1/ITPKB/FBXO7/TESC/NFATC2/TESPA1/PRKCZ/NOTCH2/PTPRC/PTK2B/LEF1/RASGRP1/PRKDC/ZFPM1
## GO:1902105                                                                                                                                                  ABL1/ZMIZ1/TGFBR2/UBASH3B/TNF/MIR145/HLX/GPR68/TREM2/LTF/IL20/IL1B/RNF41/SH3RF1/IL34/RASSF2/CD4/TRIB1/LRRC17/AGER/ADA/PIK3R6/TCF7/ADAM8/NFAM1/CBFB/CDK6/CD28/CEBPB/MITF/FOXP1/IL4/RB1/FADD/PIK3R1/ITPKB/FBXO7/TESC/NFATC2/TESPA1/PRKCZ/NOTCH2/PTPRC/LEF1/RASGRP1/PRKDC/ZFPM1
## GO:0043312                                               GM2A/DEFA4/SLPI/TARM1/CLEC5A/MPO/GDI2/SIRPA/AZU1/TNFRSF1B/DYNC1H1/ABCA13/PSMB7/FCN1/LTF/DOCK2/PRG3/DNAJC3/PSMA2/ATP11A/AMPD3/LAIR1/GLB1/RAB31/GSN/GPI/ANO6/CREG1/CD63/PLAUR/CAB39/ADAM8/NFAM1/STK10/CAP1/TMEM63A/UBR4/CRISPLD2/CLEC4C/SLC2A5/AP1M1/HK3/GYG1/ABR/CD59/DSC1/CAMP/KCNAB2/DGAT1/MCEMP1/EPX/PTPRC/PRG2/ITGAL/ARSB/COTL1/PTPRJ/RAB5C/PTAFR/GUSB/CMTM6/PGM1/CTSB/RAB37
## GO:0002283                                               GM2A/DEFA4/SLPI/TARM1/CLEC5A/MPO/GDI2/SIRPA/AZU1/TNFRSF1B/DYNC1H1/ABCA13/PSMB7/FCN1/LTF/DOCK2/PRG3/DNAJC3/PSMA2/ATP11A/AMPD3/LAIR1/GLB1/RAB31/GSN/GPI/ANO6/CREG1/CD63/PLAUR/CAB39/ADAM8/NFAM1/STK10/CAP1/TMEM63A/UBR4/CRISPLD2/CLEC4C/SLC2A5/AP1M1/HK3/GYG1/ABR/CD59/DSC1/CAMP/KCNAB2/DGAT1/MCEMP1/EPX/PTPRC/PRG2/ITGAL/ARSB/COTL1/PTPRJ/RAB5C/PTAFR/GUSB/CMTM6/PGM1/CTSB/RAB37
##            Count
## GO:0030099    71
## GO:0045637    45
## GO:1903706    68
## GO:1902105    47
## GO:0043312    64
## GO:0002283    64
barplot(ego, showCategory=20)

# based on 1509 genes and 1390 unique genes
pdf(file = file.path(sub.plots.dir, "barplot_GOBP_CRA_CAMP_overlap_genes_genomewide_thresh.pdf"),width = 7, height = 7)
barplot(ego, showCategory=20)
dev.off()
## png 
##   2
# not needed as readable=TRUE in enrichGO function
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)
## Warning: ggrepel: 10 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

p1 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)

# for CAMP
coeff.camp <- merge_CG_gw$logFC
names(coeff.camp) <- merge_CG_gw$Gene.x
coeff.camp.df <- data.frame(coeff.camp)
coeff.camp.df$Gene <- names(coeff.camp)
coeff.camp.uniq <- coeff.camp.df$Gene[!is.na(coeff.camp.df$Gene)]
coeff.camp.uniq <- coeff.camp.df[!is.na(coeff.camp.df$Gene), ]
coeff.camp.uniq <- coeff.camp.df[coeff.camp.df$Gene!="NA",]
coeff.camp.uniq <- coeff.camp.df[!duplicated(coeff.camp.df$Gene), ]

coeff.camp.uniq.v <- coeff.camp.uniq$coeff.camp
names(coeff.camp.uniq.v) <- coeff.camp.uniq$Gene
geneList <- coeff.camp.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')
## 'select()' returned 1:1 mapping between keys and columns
length(symbols.entrez)
## [1] 1509
#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 1390
## [1] 1390
ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)

ego <- enrichGO(gene          = gene,
                OrgDb         = org.Hs.eg.db,
                ont           = "BP",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.05,
                qvalueCutoff  = 0.05,
                readable      = TRUE)
dim(ego)
## [1] 251   9
head(ego)
##                    ID                                       Description
## GO:0030099 GO:0030099                      myeloid cell differentiation
## GO:0045637 GO:0045637        regulation of myeloid cell differentiation
## GO:1903706 GO:1903706                         regulation of hemopoiesis
## GO:1902105 GO:1902105           regulation of leukocyte differentiation
## GO:0043312 GO:0043312                          neutrophil degranulation
## GO:0002283 GO:0002283 neutrophil activation involved in immune response
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0030099   71/1233 431/18866 4.110661e-13 2.338144e-09 1.981339e-09
## GO:0045637   45/1233 263/18866 2.506735e-09 7.129156e-06 6.041233e-06
## GO:1903706   68/1233 498/18866 5.649299e-09 9.610415e-06 8.143847e-06
## GO:1902105   47/1233 290/18866 6.758379e-09 9.610415e-06 8.143847e-06
## GO:0043312   64/1233 487/18866 6.862848e-08 7.807176e-05 6.615786e-05
## GO:0002283   64/1233 490/18866 8.630413e-08 8.181632e-05 6.933099e-05
##                                                                                                                                                                                                                                                                                                                                                                                                                                   geneID
## GO:0030099 TGFBR2/CLEC5A/TNF/TREM2/LRRK1/APP/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/THRA/TMOD3/LRRC17/RASSF2/PIP4K2A/RNF41/ASH2L/P4HTM/EPAS1/ADD1/ADAR/EIF6/CD4/PRKCB/KMT2C/CDK6/FARP2/SETD1A/MTURN/FOXP1/TRIB1/SRC/SPI1/HDAC1/ARID4A/RARG/CBFB/CD81/KLF1/FAXDC2/CEBPB/MITF/CEBPE/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/LBR/ACTN1/SH3PXD2A/FADD/BATF2/PIK3R1/CREBBP/CDK5RAP3/KAT8/VPS33A/ITPKB/MFHAS1/TESC/HIPK2/PRKDC/IKZF1/LEF1/ZFPM1
## GO:0045637                                                                                                                                                              TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/LRRC17/RASSF2/RNF41/ASH2L/P4HTM/EIF6/CD4/PRKCB/KMT2C/CDK6/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/RARG/CBFB/FAXDC2/CEBPB/MITF/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FADD/PIK3R1/CREBBP/ITPKB/TESC/PRKDC/LEF1/ZFPM1
## GO:1903706                       TGFBR2/ABL1/ZMIZ1/TNF/TREM2/PSMB7/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/STAT1/STAT3/IL1B/IL34/PSMA2/PIK3R6/LRRC17/RASSF2/ITCH/RNF41/ASH2L/P4HTM/ADA/EIF6/CD4/PRKCB/AGER/KMT2C/CDK6/SH3RF1/NFATC2/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/PSMC1/RARG/CBFB/TCF7/FAXDC2/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FBXO7/RASGRP1/TESPA1/FADD/PIK3R1/CREBBP/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## GO:1902105                                                                                                                                                  TGFBR2/ABL1/ZMIZ1/TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/IL1B/IL34/PIK3R6/LRRC17/RASSF2/RNF41/ADA/CD4/AGER/CDK6/SH3RF1/NFATC2/FOXP1/TRIB1/CBFB/TCF7/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/RB1/IL4/FBXO7/RASGRP1/TESPA1/FADD/PIK3R1/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## GO:0043312                                               TARM1/CLEC5A/GM2A/DEFA4/AZU1/SIRPA/SLPI/MPO/GDI2/ABCA13/DYNC1H1/PSMB7/TNFRSF1B/LTF/FCN1/PRG3/DOCK2/DNAJC3/PSMA2/GLB1/AMPD3/RAB31/GPI/LAIR1/CREG1/PLAUR/ANO6/UBR4/GSN/ATP11A/CAB39/CAP1/AP1M1/STK10/CAMP/KCNAB2/CD59/CD63/GYG1/ADAM8/NFAM1/DGAT1/TMEM63A/CRISPLD2/ITGAL/CLEC4C/SLC2A5/HK3/ABR/PTPRJ/PGM1/RAB5C/DSC1/PTPRC/ARSB/EPX/RAB37/CTSB/CMTM6/MCEMP1/PRG2/PTAFR/COTL1/GUSB
## GO:0002283                                               TARM1/CLEC5A/GM2A/DEFA4/AZU1/SIRPA/SLPI/MPO/GDI2/ABCA13/DYNC1H1/PSMB7/TNFRSF1B/LTF/FCN1/PRG3/DOCK2/DNAJC3/PSMA2/GLB1/AMPD3/RAB31/GPI/LAIR1/CREG1/PLAUR/ANO6/UBR4/GSN/ATP11A/CAB39/CAP1/AP1M1/STK10/CAMP/KCNAB2/CD59/CD63/GYG1/ADAM8/NFAM1/DGAT1/TMEM63A/CRISPLD2/ITGAL/CLEC4C/SLC2A5/HK3/ABR/PTPRJ/PGM1/RAB5C/DSC1/PTPRC/ARSB/EPX/RAB37/CTSB/CMTM6/MCEMP1/PRG2/PTAFR/COTL1/GUSB
##            Count
## GO:0030099    71
## GO:0045637    45
## GO:1903706    68
## GO:1902105    47
## GO:0043312    64
## GO:0002283    64
barplot(ego, showCategory=20)

#dotplot(ego)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for GO ORA")
## wrong orderBy parameter; set to default `orderBy = "x"`

#gseaplot(y, y[1,1], title=y[1,2])

pdf(file = file.path(sub.plots.dir, "dotplot_enrichGO_CRA_CAMP.pdf"),width = 7, height = 7)
enrichplot::dotplot(ego, showCategory=20) + ggtitle("dotplot for GO ORA")
## wrong orderBy parameter; set to default `orderBy = "x"`
dev.off()
## png 
##   2
egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)
## Warning: ggrepel: 30 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

p2 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)

# for better visualizing chose nrow=2
cowplot::plot_grid(p1, p2, ncol=1, nrow=2,labels=LETTERS[1:2], rel_widths=c(.8, .8))
## Warning: ggrepel: 118 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 132 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_coeff_overlap_univ.pdf"),width = 22, height = 9)
# Genes and gene ontology enrichments network
cowplot::plot_grid(p1, p2, ncol=2, labels=LETTERS[1:2], rel_widths=c(.8, .8))
dev.off()
## png 
##   2
# Can also plot it this way as both plots would anyway look same except fold change in both datasets
# without fold change
cnetplot(ego, node_label="all", categorySize="qvalue")
## Warning: ggrepel: 26 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

# save it
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_overlap_without_coeff.pdf"),width = 11, height = 9)
# Genes and gene ontology enrichments network
cnetplot(ego, node_label="all", categorySize="qvalue")
dev.off()
## png 
##   2
# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
# the plot would look same for CRA and CAMP as you are just plotting pvalues and terms, not the effect estimates
x1 <- pairwise_termsim(ego)
emapplot(x1)

pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_enrichGO_CRA_CAMP_overlap_gw_genes.pdf"),
    width = 11, height = 9)
emapplot(x1)
dev.off()
## png 
##   2
kk <- enrichKEGG(gene         = gene,
                 organism     = 'hsa',
                 pvalueCutoff = 0.05,
                 pAdjustMethod = "BH",
                 qvalueCutoff = 0.05,
                 minGSSize = 50,
                 maxGSSize = 500)
## Reading KEGG annotation online:
## Reading KEGG annotation online:
dim(kk) #28
## [1] 29  9
kk.ge <- setReadable(kk, 'org.Hs.eg.db', 'ENTREZID')
head(kk.ge)
##                ID                                      Description GeneRatio
## hsa04070 hsa04070            Phosphatidylinositol signaling system    24/620
## hsa04921 hsa04921                       Oxytocin signaling pathway    28/620
## hsa04725 hsa04725                              Cholinergic synapse    21/620
## hsa04750 hsa04750 Inflammatory mediator regulation of TRP channels    19/620
## hsa04371 hsa04371                         Apelin signaling pathway    23/620
## hsa00562 hsa00562                    Inositol phosphate metabolism    15/620
##           BgRatio       pvalue     p.adjust       qvalue
## hsa04070  97/8113 1.707659e-07 3.978845e-05 2.876057e-05
## hsa04921 154/8113 1.255423e-05 1.462568e-03 1.057198e-03
## hsa04725 113/8113 1.091982e-04 7.481291e-03 5.407755e-03
## hsa04750  98/8113 1.284342e-04 7.481291e-03 5.407755e-03
## hsa04371 139/8113 3.196988e-04 1.286082e-02 9.296278e-03
## hsa00562  73/8113 3.356060e-04 1.286082e-02 9.296278e-03
##                                                                                                                                                                                          geneID
## hsa04070                               ITPR2/SYNJ2/PIK3C2B/ITPKC/CALML4/PTEN/PI4KA/INPP5F/PIP4K2A/PIP5K1B/PRKCB/PI4KB/PIK3CB/DGKI/IP6K2/ITPK1/INPP5A/CALM1/DGKG/PIK3R1/ITPKB/INPP4A/ITPR1/MTMR3
## hsa04921 CAMKK2/ITPR2/ADCY9/CACNA2D2/CALML4/GNAQ/MYLK4/PIK3R6/KCNJ6/MAP2K5/CACNA2D1/PRKCB/CACNA1S/NFATC2/PRKAG2/CAMK1D/SRC/CACNA1D/MYLK/PRKAB1/PIK3R5/MYL9/CALM1/EEF2K/GNAO1/CAMK2G/ITPR1/MYLK3
## hsa04725                                                  ITPR2/ADCY9/CREB3L4/GNG7/GNAQ/CREB3L2/PIK3R6/KCNJ6/CHRM1/PRKCB/CACNA1S/PIK3CB/GNG12/CACNA1D/GNB5/PIK3R5/PIK3R1/FYN/GNAO1/CAMK2G/ITPR1
## hsa04750                                                                      NGF/ITPR2/ADCY9/CALML4/IL1B/GNAQ/PRKCE/BDKRB2/PRKCB/MAPK13/PIK3CB/SRC/ASIC1/P2RY2/CALM1/PIK3R1/CAMK2G/ITPR1/PRKCH
## hsa04371                                           ITPR2/ADCY9/CALML4/GNG7/GNAQ/MYLK4/PIK3R6/PRKCE/GNG12/PRKAG2/MYLK/PRKAB1/GNB5/PIK3R5/JAG1/CALM1/MAP1LC3B2/MEF2D/HDAC4/SPHK2/ITPR1/CDH1/MYLK3
## hsa00562                                                                                     SYNJ2/PIK3C2B/ITPKC/PTEN/PI4KA/INPP5F/PIP4K2A/PIP5K1B/PI4KB/PIK3CB/ITPK1/INPP5A/ITPKB/INPP4A/MTMR3
##          Count
## hsa04070    24
## hsa04921    28
## hsa04725    21
## hsa04750    19
## hsa04371    23
## hsa00562    15
# shows all enriched KEGG terms
kk.ge@result$Description
##   [1] "Phosphatidylinositol signaling system"                        
##   [2] "Oxytocin signaling pathway"                                   
##   [3] "Cholinergic synapse"                                          
##   [4] "Inflammatory mediator regulation of TRP channels"             
##   [5] "Apelin signaling pathway"                                     
##   [6] "Inositol phosphate metabolism"                                
##   [7] "Dopaminergic synapse"                                         
##   [8] "Kaposi sarcoma-associated herpesvirus infection"              
##   [9] "Aldosterone synthesis and secretion"                          
##  [10] "Insulin resistance"                                           
##  [11] "Calcium signaling pathway"                                    
##  [12] "Axon guidance"                                                
##  [13] "Human cytomegalovirus infection"                              
##  [14] "cGMP-PKG signaling pathway"                                   
##  [15] "Adherens junction"                                            
##  [16] "Platelet activation"                                          
##  [17] "Hepatitis B"                                                  
##  [18] "Insulin signaling pathway"                                    
##  [19] "Sphingolipid signaling pathway"                               
##  [20] "Glioma"                                                       
##  [21] "AMPK signaling pathway"                                       
##  [22] "GnRH signaling pathway"                                       
##  [23] "Gastric acid secretion"                                       
##  [24] "T cell receptor signaling pathway"                            
##  [25] "Lysosome"                                                     
##  [26] "Endocytosis"                                                  
##  [27] "Focal adhesion"                                               
##  [28] "Amphetamine addiction"                                        
##  [29] "Chemokine signaling pathway"                                  
##  [30] "Cellular senescence"                                          
##  [31] "Yersinia infection"                                           
##  [32] "Osteoclast differentiation"                                   
##  [33] "Growth hormone synthesis, secretion and action"               
##  [34] "Hepatocellular carcinoma"                                     
##  [35] "Melanogenesis"                                                
##  [36] "Human immunodeficiency virus 1 infection"                     
##  [37] "Viral carcinogenesis"                                         
##  [38] "Serotonergic synapse"                                         
##  [39] "Renin secretion"                                              
##  [40] "Renal cell carcinoma"                                         
##  [41] "Glucagon signaling pathway"                                   
##  [42] "Glycerolipid metabolism"                                      
##  [43] "GABAergic synapse"                                            
##  [44] "Rap1 signaling pathway"                                       
##  [45] "Endocrine and other factor-regulated calcium reabsorption"    
##  [46] "HIF-1 signaling pathway"                                      
##  [47] "Neurotrophin signaling pathway"                               
##  [48] "AGE-RAGE signaling pathway in diabetic complications"         
##  [49] "Adrenergic signaling in cardiomyocytes"                       
##  [50] "Autophagy - animal"                                           
##  [51] "FoxO signaling pathway"                                       
##  [52] "Shigellosis"                                                  
##  [53] "TNF signaling pathway"                                        
##  [54] "Cortisol synthesis and secretion"                             
##  [55] "Vascular smooth muscle contraction"                           
##  [56] "Regulation of actin cytoskeleton"                             
##  [57] "C-type lectin receptor signaling pathway"                     
##  [58] "Cushing syndrome"                                             
##  [59] "Carbon metabolism"                                            
##  [60] "Pancreatic cancer"                                            
##  [61] "Glycolysis / Gluconeogenesis"                                 
##  [62] "Cell cycle"                                                   
##  [63] "Fc gamma R-mediated phagocytosis"                             
##  [64] "Circadian entrainment"                                        
##  [65] "Prostate cancer"                                              
##  [66] "Fc epsilon RI signaling pathway"                              
##  [67] "Estrogen signaling pathway"                                   
##  [68] "Notch signaling pathway"                                      
##  [69] "Longevity regulating pathway"                                 
##  [70] "Hypertrophic cardiomyopathy"                                  
##  [71] "Thyroid hormone signaling pathway"                            
##  [72] "Spinocerebellar ataxia"                                       
##  [73] "Non-small cell lung cancer"                                   
##  [74] "Wnt signaling pathway"                                        
##  [75] "Leukocyte transendothelial migration"                         
##  [76] "GnRH secretion"                                               
##  [77] "Inflammatory bowel disease"                                   
##  [78] "Parathyroid hormone synthesis, secretion and action"          
##  [79] "Insulin secretion"                                            
##  [80] "Chronic myeloid leukemia"                                     
##  [81] "Relaxin signaling pathway"                                    
##  [82] "Bacterial invasion of epithelial cells"                       
##  [83] "Long-term potentiation"                                       
##  [84] "Acute myeloid leukemia"                                       
##  [85] "Human papillomavirus infection"                               
##  [86] "Glycerophospholipid metabolism"                               
##  [87] "Endometrial cancer"                                           
##  [88] "Oocyte meiosis"                                               
##  [89] "PD-L1 expression and PD-1 checkpoint pathway in cancer"       
##  [90] "Ras signaling pathway"                                        
##  [91] "VEGF signaling pathway"                                       
##  [92] "Biosynthesis of cofactors"                                    
##  [93] "mTOR signaling pathway"                                       
##  [94] "N-Glycan biosynthesis"                                        
##  [95] "Amoebiasis"                                                   
##  [96] "Tuberculosis"                                                 
##  [97] "Salivary secretion"                                           
##  [98] "Longevity regulating pathway - multiple species"              
##  [99] "Lysine degradation"                                           
## [100] "ErbB signaling pathway"                                       
## [101] "Dilated cardiomyopathy"                                       
## [102] "Thyroid hormone synthesis"                                    
## [103] "Colorectal cancer"                                            
## [104] "cAMP signaling pathway"                                       
## [105] "Ubiquitin mediated proteolysis"                               
## [106] "Alcoholic liver disease"                                      
## [107] "Endocrine resistance"                                         
## [108] "MAPK signaling pathway"                                       
## [109] "Fatty acid metabolism"                                        
## [110] "EGFR tyrosine kinase inhibitor resistance"                    
## [111] "Breast cancer"                                                
## [112] "Adipocytokine signaling pathway"                              
## [113] "Pancreatic secretion"                                         
## [114] "Chagas disease"                                               
## [115] "Morphine addiction"                                           
## [116] "Phospholipase D signaling pathway"                            
## [117] "Retrograde endocannabinoid signaling"                         
## [118] "Glutamatergic synapse"                                        
## [119] "Th1 and Th2 cell differentiation"                             
## [120] "Small cell lung cancer"                                       
## [121] "Prolactin signaling pathway"                                  
## [122] "PI3K-Akt signaling pathway"                                   
## [123] "Human T-cell leukemia virus 1 infection"                      
## [124] "Melanoma"                                                     
## [125] "Alcoholism"                                                   
## [126] "Chemical carcinogenesis - receptor activation"                
## [127] "MicroRNAs in cancer"                                          
## [128] "Epstein-Barr virus infection"                                 
## [129] "Transcriptional misregulation in cancer"                      
## [130] "Hippo signaling pathway"                                      
## [131] "Gap junction"                                                 
## [132] "Leishmaniasis"                                                
## [133] "Arrhythmogenic right ventricular cardiomyopathy"              
## [134] "Influenza A"                                                  
## [135] "Progesterone-mediated oocyte maturation"                      
## [136] "Salmonella infection"                                         
## [137] "Pathways of neurodegeneration - multiple diseases"            
## [138] "B cell receptor signaling pathway"                            
## [139] "Proteoglycans in cancer"                                      
## [140] "Long-term depression"                                         
## [141] "Viral myocarditis"                                            
## [142] "Hepatitis C"                                                  
## [143] "NOD-like receptor signaling pathway"                          
## [144] "Choline metabolism in cancer"                                 
## [145] "Malaria"                                                      
## [146] "Basal cell carcinoma"                                         
## [147] "Toxoplasmosis"                                                
## [148] "Purine metabolism"                                            
## [149] "Bile secretion"                                               
## [150] "Fluid shear stress and atherosclerosis"                       
## [151] "Protein digestion and absorption"                             
## [152] "Alzheimer disease"                                            
## [153] "Signaling pathways regulating pluripotency of stem cells"     
## [154] "Drug metabolism - other enzymes"                              
## [155] "Hedgehog signaling pathway"                                   
## [156] "TGF-beta signaling pathway"                                   
## [157] "IL-17 signaling pathway"                                      
## [158] "Peroxisome"                                                   
## [159] "Central carbon metabolism in cancer"                          
## [160] "Glutathione metabolism"                                       
## [161] "mRNA surveillance pathway"                                    
## [162] "Apoptosis"                                                    
## [163] "Gastric cancer"                                               
## [164] "JAK-STAT signaling pathway"                                   
## [165] "Complement and coagulation cascades"                          
## [166] "Lipid and atherosclerosis"                                    
## [167] "Neutrophil extracellular trap formation"                      
## [168] "Hematopoietic cell lineage"                                   
## [169] "Viral protein interaction with cytokine and cytokine receptor"
## [170] "Cardiac muscle contraction"                                   
## [171] "Arachidonic acid metabolism"                                  
## [172] "Biosynthesis of amino acids"                                  
## [173] "Prion disease"                                                
## [174] "Tight junction"                                               
## [175] "Cholesterol metabolism"                                       
## [176] "Toll-like receptor signaling pathway"                         
## [177] "Natural killer cell mediated cytotoxicity"                    
## [178] "Ovarian steroidogenesis"                                      
## [179] "Synaptic vesicle cycle"                                       
## [180] "Th17 cell differentiation"                                    
## [181] "Measles"                                                      
## [182] "RIG-I-like receptor signaling pathway"                        
## [183] "Regulation of lipolysis in adipocytes"                        
## [184] "Non-alcoholic fatty liver disease"                            
## [185] "Huntington disease"                                           
## [186] "Mitophagy - animal"                                           
## [187] "Platinum drug resistance"                                     
## [188] "Cytokine-cytokine receptor interaction"                       
## [189] "Mineral absorption"                                           
## [190] "PPAR signaling pathway"                                       
## [191] "NF-kappa B signaling pathway"                                 
## [192] "Diabetic cardiomyopathy"                                      
## [193] "Pertussis"                                                    
## [194] "Thermogenesis"                                                
## [195] "Cytosolic DNA-sensing pathway"                                
## [196] "Rheumatoid arthritis"                                         
## [197] "Cysteine and methionine metabolism"                           
## [198] "Protein processing in endoplasmic reticulum"                  
## [199] "Necroptosis"                                                  
## [200] "Drug metabolism - cytochrome P450"                            
## [201] "ECM-receptor interaction"                                     
## [202] "Cell adhesion molecules"                                      
## [203] "Legionellosis"                                                
## [204] "Pyrimidine metabolism"                                        
## [205] "Steroid hormone biosynthesis"                                 
## [206] "Antigen processing and presentation"                          
## [207] "Staphylococcus aureus infection"                              
## [208] "Chemical carcinogenesis - reactive oxygen species"            
## [209] "Aminoacyl-tRNA biosynthesis"                                  
## [210] "Pathogenic Escherichia coli infection"                        
## [211] "Chemical carcinogenesis - DNA adducts"                        
## [212] "Arginine and proline metabolism"                              
## [213] "Epithelial cell signaling in Helicobacter pylori infection"   
## [214] "Parkinson disease"                                            
## [215] "Autoimmune thyroid disease"                                   
## [216] "p53 signaling pathway"                                        
## [217] "Metabolism of xenobiotics by cytochrome P450"                 
## [218] "RNA degradation"                                              
## [219] "Nucleocytoplasmic transport"                                  
## [220] "Retinol metabolism"                                           
## [221] "Ribosome biogenesis in eukaryotes"                            
## [222] "Amyotrophic lateral sclerosis"                                
## [223] "Vibrio cholerae infection"                                    
## [224] "Coronavirus disease - COVID-19"                               
## [225] "Fanconi anemia pathway"                                       
## [226] "Phagosome"                                                    
## [227] "Systemic lupus erythematosus"                                 
## [228] "Spliceosome"                                                  
## [229] "Taste transduction"                                           
## [230] "Neuroactive ligand-receptor interaction"                      
## [231] "Oxidative phosphorylation"                                    
## [232] "Herpes simplex virus 1 infection"                             
## [233] "Olfactory transduction"
save(kk.ge, file=file.path(res.dir,
                  paste0("enrich_Kegg_CRA_CAMP_genomewide_thresh_", timeStamp, ".RData")))

write.table(kk.ge@result,file=file.path(res.dir, 
       paste0("enrichKegg_CRA_CAMP_gw_thresh_",timeStamp,".txt"))
                ,sep="\t",row.names=F,quote=F)

browseKEGG(kk, 'hsa04070')
library("pathview")
## ##############################################################################
## Pathview is an open source software package distributed under GNU General
## Public License version 3 (GPLv3). Details of GPLv3 is available at
## http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
## formally cite the original Pathview paper (not just mention it) in publications
## or products. For details, do citation("pathview") within R.
## 
## The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
## license agreement (details at http://www.kegg.jp/kegg/legal.html).
## ##############################################################################
hsa04070 <- pathview(gene.data  = geneList,
                     pathway.id = "hsa04070",
                     species    = "hsa",
                     limit      = list(gene=max(abs(geneList)), cpd=1))
## 'select()' returned 1:1 mapping between keys and columns
## Info: Working in directory /udd/reprk/projects/TOPMed/scripts
## Info: Writing image file hsa04070.pathview.png
file.copy("hsa04070.pathview.png", sub.plots.dir)
## [1] FALSE
#eg2np <- bitr_kegg(gene, fromType='kegg', toType='ncbi-geneid', organism='hsa')

geneList.na <- geneList[names(geneList)!="NA"]
kk2 <- gseKEGG(geneList     = geneList.na,
               organism     = 'hsa',
               minGSSize    = 50,
               pvalueCutoff = 0.05,
               pAdjustMethod = "BH",
               maxGSSize = 500,
               by = "fgsea",
               verbose      = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
head(kk2)
## [1] ID              Description     setSize         enrichmentScore
## [5] NES             pvalue          p.adjust        qvalues        
## <0 rows> (or 0-length row.names)
#preparing geneSet collections...
#GSEA analysis...
#no term enriched under specific pvalueCutoff...

# GSEA , no enrichment
ego.gse <- gseGO(geneList     = geneList.na,
              OrgDb        = org.Hs.eg.db,
              ont          = "BP",
              minGSSize    = 50,
              maxGSSize    = 500,
              pvalueCutoff = 0.05,
              pAdjustMethod = "BH",
              verbose      = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
# H and C2,3,5,7,8
# Gene set enrichment analysis
msigdbr_show_species()
## Warning: 'msigdbr_show_species' is deprecated.
## Use 'msigdbr_species' instead.
## See help("Deprecated")
##  [1] "Anolis carolinensis"             "Bos taurus"                     
##  [3] "Caenorhabditis elegans"          "Canis lupus familiaris"         
##  [5] "Danio rerio"                     "Drosophila melanogaster"        
##  [7] "Equus caballus"                  "Felis catus"                    
##  [9] "Gallus gallus"                   "Homo sapiens"                   
## [11] "Macaca mulatta"                  "Monodelphis domestica"          
## [13] "Mus musculus"                    "Ornithorhynchus anatinus"       
## [15] "Pan troglodytes"                 "Rattus norvegicus"              
## [17] "Saccharomyces cerevisiae"        "Schizosaccharomyces pombe 972h-"
## [19] "Sus scrofa"                      "Xenopus tropicalis"
m_df <- msigdbr(species = "Homo sapiens")
head(m_df, 2) %>% as.data.frame
##   gs_cat      gs_subcat        gs_name gene_symbol entrez_gene    ensembl_gene
## 1     C3 MIR:MIR_Legacy AAACCAC_MIR140       ABCC4       10257 ENSG00000125257
## 2     C3 MIR:MIR_Legacy AAACCAC_MIR140    ABRAXAS2       23172 ENSG00000165660
##   human_gene_symbol human_entrez_gene human_ensembl_gene  gs_id gs_pmid
## 1             ABCC4             10257    ENSG00000125257 M12609        
## 2          ABRAXAS2             23172    ENSG00000165660 M12609        
##   gs_geoid gs_exact_source gs_url
## 1                                
## 2                                
##                                                                                                                                                                                           gs_description
## 1 Genes having at least one occurence of the motif AAACCAC in their 3' untranslated region. The motif represents putative target (that is, seed match) of human mature miRNA hsa-miR-140 (v7.1 miRBase).
## 2 Genes having at least one occurence of the motif AAACCAC in their 3' untranslated region. The motif represents putative target (that is, seed match) of human mature miRNA hsa-miR-140 (v7.1 miRBase).
# Pulling data from msigdbr
# hallmark gene sets
m_H <- msigdbr(species = "Homo sapiens", category = "H") %>% 
    dplyr::select(gs_name, entrez_gene)

# curated gene sets
m_C2 <- msigdbr(species = "Homo sapiens", category = "C2") %>% 
    dplyr::select(gs_name, entrez_gene)

# regulatory target/motif gene sets
m_C3 <- msigdbr(species = "Homo sapiens", category = "C3") %>% 
    dplyr::select(gs_name, entrez_gene)

# ontology gene sets
m_C5 <- msigdbr(species = "Homo sapiens", category = "C5") %>% 
    dplyr::select(gs_name, entrez_gene)

# immunologic signature gene sets
m_C7 <- msigdbr(species = "Homo sapiens", category = "C7") %>% 
    dplyr::select(gs_name, entrez_gene)

# cell type signature gene sets
m_C8 <- msigdbr(species = "Homo sapiens", category = "C8") %>% 
    dplyr::select(gs_name, entrez_gene)

# enrichments
em.H <- enricher(gene, TERM2GENE=m_H, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # not sig
dim(em.H)
## [1] 0 9
em.C2 <- enricher(gene, TERM2GENE=m_C2, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 563
em.C2.ge <- setReadable(em.C2, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C2.ge)
## [1] 563   9
head(em.C2.ge)
##                                                                                        ID
## MARTENS_BOUND_BY_PML_RARA_FUSION                         MARTENS_BOUND_BY_PML_RARA_FUSION
## GRYDER_PAX3FOXO1_TOP_ENHANCERS                             GRYDER_PAX3FOXO1_TOP_ENHANCERS
## ZHENG_BOUND_BY_FOXP3                                                 ZHENG_BOUND_BY_FOXP3
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY                         WP_VEGFAVEGFR2_SIGNALING_PATHWAY
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN             THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP
##                                                                               Description
## MARTENS_BOUND_BY_PML_RARA_FUSION                         MARTENS_BOUND_BY_PML_RARA_FUSION
## GRYDER_PAX3FOXO1_TOP_ENHANCERS                             GRYDER_PAX3FOXO1_TOP_ENHANCERS
## ZHENG_BOUND_BY_FOXP3                                                 ZHENG_BOUND_BY_FOXP3
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY                         WP_VEGFAVEGFR2_SIGNALING_PATHWAY
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN             THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP
##                                              GeneRatio   BgRatio       pvalue
## MARTENS_BOUND_BY_PML_RARA_FUSION               89/1333 455/21697 7.945626e-23
## GRYDER_PAX3FOXO1_TOP_ENHANCERS                 71/1333 441/21697 7.264148e-14
## ZHENG_BOUND_BY_FOXP3                           75/1333 495/21697 3.467969e-13
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY               68/1333 438/21697 1.421528e-12
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN         43/1333 227/21697 3.222204e-11
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP   61/1333 412/21697 1.495306e-10
##                                                  p.adjust       qvalue
## MARTENS_BOUND_BY_PML_RARA_FUSION             3.883822e-19 2.993410e-19
## GRYDER_PAX3FOXO1_TOP_ENHANCERS               1.775358e-10 1.368336e-10
## ZHENG_BOUND_BY_FOXP3                         5.650478e-10 4.355040e-10
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY             1.737107e-09 1.338855e-09
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN       3.150026e-08 2.427846e-08
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 1.218176e-07 9.388948e-08
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         geneID
## MARTENS_BOUND_BY_PML_RARA_FUSION             ZMIZ1/CUX1/UCK2/CELF2/SIRPA/RHBDF2/ITPR2/ANKRD11/UBASH3B/TPD52L2/FCN1/PTEN/HNRNPM/PITPNM2/KLHL24/WNT5B/IQCD/ST3GAL2/ABHD2/RAB31/NCOR2/CCDC174/CHST15/SLC24A3/ALOX5AP/ACSL1/IQSEC1/PREX1/HCK/PIGL/PAFAH2/SPI1/RAB20/RPS6KA2/GSE1/PHF12/RNF122/NOLC1/GAS7/GALC/EFHD2/PIK3AP1/KCNAB2/NDRG1/RAB11FIP1/GNB5/ANKRD33B/ADAM8/ALDH2/PEBP4/MYO9B/POC1A/RNF34/MBD6/TBXAS1/UBE2O/WDR81/CDH23/P2RY2/ADORA3/LBR/RAP1GAP2/TMEM104/PXN/FAM53B/RAPGEF1/DENND3/SH3PXD2A/SULF2/MEF2D/PTPRJ/HDAC4/SPTBN1/NADK/GALNT6/SPHK2/GFOD1/RAB37/CAMK2G/ACP5/TESC/ITPR1/LRRC20/MGLL/CAPG/COTL1/DAPK2/GUSB/KSR1
## GRYDER_PAX3FOXO1_TOP_ENHANCERS                                                                                                                                      CELF2/TNS3/PPM1H/CHST11/GDI2/ADCY9/TGOLN2/ADAM19/APP/RBM20/ARHGEF10/JARID2/ANKRD13A/CLASP1/MFSD2A/HMGXB4/CHCHD3/PARK7/COL4A1/MCC/OPA1/ZEB2/SPATS2L/COPS3/NR3C1/VTI1A/SUDS3/MAN1C1/CEP128/MED13L/NCOR2/UBAC2/CHST15/SLC24A3/ALOX5AP/SNX29/CD9/PLXNA2/POR/PREX1/ARHGAP26/GSE1/CAP1/NOLC1/EFHD2/NOTCH2/ADAMTS14/MYO9B/CSRP1/SLC7A1/MCM2/LRIG1/ELMO1/USP15/RAPGEF1/RERE/CTNNBL1/EEF2K/SULF2/STIM2/SASH1/CREBBP/ITPKB/TRAP1/GGA2/TLE3/FYN/GRB10/MSI2/DAPK1/SNX9
## ZHENG_BOUND_BY_FOXP3                                                                                                                               TGFBR2/CELF2/MGAT5/TRIM27/PPP2R5C/GDI2/ITPR2/OPRM1/SSH2/ADAM19/ANKRD11/UBASH3B/ARHGEF10/JARID2/EXT1/PARK7/ZNRF1/HECTD1/LRRC8C/IL10RB/SRPK1/PIP4K2A/VGLL4/ZNF175/PDE4B/UST/AGPS/PHTF2/LDLRAD4/ABTB2/UBAC2/DENND5A/STAT4/THADA/FOXP1/LCP1/TRIB1/STK10/IKZF2/RAB19/SAG/EPS15L1/TET3/EPB41/IBTK/RBL2/CD28/NCK2/PEBP4/PTK2B/INTS9/AKAP13/RB1/MAP4K4/GPD2/LRIG1/SGMS1/XXYLT1/ELMO1/CYTH1/HK3/TESPA1/MUC20/PTPRC/SPTBN1/VOPP1/FYN/TBC1D5/GPHN/CDK17/MAP3K1/LEF1/SNX9/PRKCH/SLC23A2
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY                                                                                                                                                                                    CAMKK2/ABL1/VAV2/TPP1/ACACA/MKNK1/CCRL2/HLX/STAT1/STAT3/KL/HDAC9/EPHB2/CDC42BPB/TMOD3/SRPK1/ITCH/NAPA/EPS15/CAPZB/VPS39/MICAL2/PTPN1/CACNA2D1/PRKCE/TPCN2/PRKCB/TNXB/SIAH2/BRD4/PLAUR/NFATC2/GRB2/SRC/NOTCH4/HDAC1/LRRC59/BSG/CHAC1/CAPN2/EPB41/NDRG1/TPM3/PTK2B/CSRP1/SLC7A1/ERG/JAG1/LDB2/TKT/TMOD1/PXN/EIF4G2/MLST8/RAPGEF1/FADD/PTPRJ/FHL2/PIK3R1/CREBBP/DSC1/HDAC4/FYN/GRB10/RAB37/PRKCZ/SLC25A25/ENG
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN                                                                                                                                                                                                                                                                                                                       CELF2/TRIM27/UBN1/GDI2/LRRFIP1/RALBP1/RALY/SRPK2/DOCK2/GNAQ/TOPBP1/PPFIA1/CAPZB/TGFA/FKBP1A/PRKCB/PNN/ACTN4/ARID4A/PHKB/GAS7/RBL2/MYO9B/TKT/CALM1/LBR/CYTH1/USP15/EIF4G2/ACTN1/RERE/ENTPD1/SLC19A1/FADD/SELPLG/NCF4/CREBBP/ITPKB/GNAO1/CAMK2G/MTMR3/DAPK2/SLC23A2
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP                                                                                                                                                                                                  NEDD9/EPB41L3/CLEC5A/SLC7A7/GM2A/TNS3/SPARC/PCK2/CCRL2/CPM/FCN1/TMEM51/CALML4/STAT1/PHACTR1/ACO1/IL1B/PACSIN2/HDAC9/TRAF3/NPL/SLC7A11/SLC36A1/BCAT1/DHCR24/PRKCB/TBC1D1/LAIR1/CHST15/IDO1/CD9/LTBP2/RAB20/TLE4/CD81/GALC/RSAD2/NDRG1/CD63/CCL18/MITF/NOTCH2/ITPK1/ST3GAL1/ITGAL/GPD2/SGMS1/RAP1GAP2/RERE/DENND3/ENTPD1/OSBPL1A/KCNMA1/MFHAS1/FYN/HK2/MAN2A2/ACP5/CTSB/ITPR1/FBP1
##                                              Count
## MARTENS_BOUND_BY_PML_RARA_FUSION                89
## GRYDER_PAX3FOXO1_TOP_ENHANCERS                  71
## ZHENG_BOUND_BY_FOXP3                            75
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY                68
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN          43
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP    61
em.C3 <- enricher(gene, TERM2GENE=m_C3, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 1522
em.C3.ge <- setReadable(em.C3, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C3.ge)
## [1] 1522    9
head(em.C3.ge)
##                                          ID           Description GeneRatio
## MIR149_3P                         MIR149_3P             MIR149_3P   63/1362
## MIR6883_5P                       MIR6883_5P            MIR6883_5P   60/1362
## MIR4441                             MIR4441               MIR4441   48/1362
## MIR6722_3P                       MIR6722_3P            MIR6722_3P   35/1362
## EBNA1BP2_TARGET_GENES EBNA1BP2_TARGET_GENES EBNA1BP2_TARGET_GENES   52/1362
## MIR4755_5P                       MIR4755_5P            MIR4755_5P   49/1362
##                         BgRatio       pvalue     p.adjust       qvalue
## MIR149_3P             435/28103 7.690761e-15 2.372777e-11 1.083485e-11
## MIR6883_5P            407/28103 1.510361e-14 2.372777e-11 1.083485e-11
## MIR4441               296/28103 1.840739e-13 1.927868e-10 8.803255e-11
## MIR6722_3P            183/28103 2.795053e-12 2.195514e-09 1.002542e-09
## EBNA1BP2_TARGET_GENES 373/28103 7.637394e-12 4.799338e-09 2.191530e-09
## MIR4755_5P            365/28103 1.181133e-10 6.185198e-08 2.824357e-08
##                                                                                                                                                                                                                                                                                                                                                                                                                               geneID
## MIR149_3P             XYLT1/TRIM67/IFFO2/PIK3C2B/KIF21B/TNS1/SUFU/RALB/ATP2A3/HK1/PITPNM2/RFT1/HMGXB3/PEX2/CREB3L2/ERI3/FAIM2/GGCX/CAPZB/DESI1/DEPDC5/NCOR2/COL11A2/SLC22A23/RSPO4/AGPAT1/TPCN1/SREBF2/FOXK1/IQSEC1/YWHAQ/SLC12A4/RPS6KA2/FAM131B/ARNT2/RTN3/ASIC1/TET3/MDM4/MINK1/RPH3AL/RNF24/SLC7A1/SH3GL1/RASSF5/CSDE1/MTA2/UNC5B/RAP1GAP2/TMEM104/SSBP3/SDC3/MEF2D/PTPRJ/STIM1/SOGA1/ANKRD52/NGFR/RAB37/AHDC1/GNAO1/HIPK2/TTYH3
## MIR6883_5P                            XYLT1/TRIM67/IFFO2/PIK3C2B/KIF21B/TNS1/SUFU/RALB/ATP2A3/HK1/PITPNM2/RFT1/HMGXB3/CREB3L2/ERI3/FAIM2/GGCX/CAPZB/DESI1/DEPDC5/NCOR2/COL11A2/SLC22A23/RSPO4/AGPAT1/TPCN1/SREBF2/FOXK1/IQSEC1/YWHAQ/SLC12A4/RPS6KA2/FAM131B/ARNT2/RTN3/ASIC1/TET3/MINK1/RPH3AL/RNF24/SLC7A1/SH3GL1/RASSF5/CSDE1/MTA2/UNC5B/RAP1GAP2/TMEM104/SSBP3/SDC3/MEF2D/PTPRJ/STIM1/SOGA1/ANKRD52/NGFR/AHDC1/GNAO1/HIPK2/TTYH3
## MIR4441                                                                                                                LRRC27/TPP1/OPRM1/ADAM19/SYNJ2/IFFO2/MYO18A/SUFU/ZBTB34/ZNRF1/MYLK4/SAMD4B/RAB3B/TOM1L2/ZDHHC3/CAPZB/LARP1/SLC41A1/NXF1/CSNK1D/ABHD2/ERC1/RPH3A/COL11A2/PLXNA2/FOXK1/MTUS2/TET3/ADARB1/MITF/ZNF70/SLC7A6/NFAM1/RNF24/APBA2/RCC2/P2RY2/ELMO1/RAP1GAP2/RAPGEF1/PCYT1A/SDC3/MEF2D/SOGA1/SLC4A5/GNAO1/FADS2/IKZF1
## MIR6722_3P                                                                                                                                                                                    TGFBR2/ADCY9/RBM20/KIF21B/GRAMD1B/RNF157/SIPA1L3/XPO7/CREB3L2/AAK1/LHPP/SNX21/C16orf70/C19orf54/CHST15/TXNRD2/NFATC2/TMEM201/RYBP/IP6K2/ARNT2/EFHD2/NFAM1/ITGAL/RERE/UPP2/TRAPPC9/SH3PXD2A/MEF2D/ITPKB/SOGA1/AHDC1/CAMK2G/LRRC20/TTYH3
## EBNA1BP2_TARGET_GENES                                                           CUX1/SLC25A37/ITPR2/MOK/ASB1/CACNA2D2/IL20/MTHFD2/HECTD1/TRANK1/SLC2A9/XPO7/UBE2D3/ERI3/INPP5F/CAMKMT/NT5DC3/VTI1A/HCFC1R1/IFT27/LAIR1/IDO1/TXNRD2/CLSTN3/AHNAK/ABCB9/FARP2/SRC/CACNA1D/ACTN4/DIDO1/LAMB1/ABCC1/DNAJC6/RSAD2/DAG1/IGF1R/C16orf72/ENO3/C11orf24/UXS1/SEMA4D/GPATCH1/STIM1/ITPKB/TNFAIP8/PTPRS/LOC101927851/AKAP1/TTC7A/ZBTB48/SLC23A2
## MIR4755_5P                                                                                                           TGFBR2/LPP/FBN2/CELF2/ZNF148/ZDHHC14/AFAP1/JARID2/ANKRD13A/RAD21/GNAQ/EPHB2/WDFY2/TMOD3/NR3C1/AK2/ERC1/GSTM3/MTCL1/PI4KB/RSPO4/ANO6/PIK3CB/PLXNA2/GNG12/CAMK1D/SPOP/IKZF2/EPHA4/MGAT3/ENTHD1/CTIF/SNAP47/BCL7A/C16orf72/MLXIP/SLC7A14/CDYL2/CHN2/CCNY/NCOA7/SH3PXD2A/DGKG/KLHL6/KCNMA1/MAN2A2/RREB1/ITPR1/YPEL2
##                       Count
## MIR149_3P                63
## MIR6883_5P               60
## MIR4441                  48
## MIR6722_3P               35
## EBNA1BP2_TARGET_GENES    52
## MIR4755_5P               49
em.C5 <- enricher(gene, TERM2GENE=m_C5, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 352
em.C5.ge <- setReadable(em.C5, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C5.ge)
## [1] 352   9
head(em.C5.ge)
##                                                                                              ID
## GOBP_MYELOID_CELL_DIFFERENTIATION                             GOBP_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_HEMOPOIESIS                                   GOBP_REGULATION_OF_HEMOPOIESIS
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION       GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM                       HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                 GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
##                                                                                     Description
## GOBP_MYELOID_CELL_DIFFERENTIATION                             GOBP_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_HEMOPOIESIS                                   GOBP_REGULATION_OF_HEMOPOIESIS
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION       GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM                       HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                 GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
##                                                 GeneRatio   BgRatio
## GOBP_MYELOID_CELL_DIFFERENTIATION                 70/1264 419/19303
## GOBP_REGULATION_OF_HEMOPOIESIS                    62/1264 415/19303
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION   45/1264 258/19303
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION      45/1264 279/19303
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM              64/1264 476/19303
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY           64/1264 480/19303
##                                                       pvalue     p.adjust
## GOBP_MYELOID_CELL_DIFFERENTIATION               3.364283e-13 3.046359e-09
## GOBP_REGULATION_OF_HEMOPOIESIS                  8.695077e-10 3.936696e-06
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 1.433888e-09 4.327953e-06
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION    1.751493e-08 3.964943e-05
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM            3.142373e-08 5.690837e-05
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY         4.319327e-08 6.518585e-05
##                                                       qvalue
## GOBP_MYELOID_CELL_DIFFERENTIATION               2.587665e-09
## GOBP_REGULATION_OF_HEMOPOIESIS                  3.343944e-06
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 3.676288e-06
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION    3.367937e-05
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM            4.833962e-05
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY         5.537074e-05
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                 geneID
## GOBP_MYELOID_CELL_DIFFERENTIATION               TGFBR2/TNF/TREM2/LRRK1/APP/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/THRA/TMOD3/LRRC17/RASSF2/PIP4K2A/RNF41/ASH2L/P4HTM/EPAS1/ADD1/ADAR/EIF6/CD4/PRKCB/KMT2C/CDK6/FARP2/SETD1A/MTURN/FOXP1/TRIB1/SRC/SPI1/HDAC1/ARID4A/RARG/CBFB/CD81/KLF1/FAXDC2/CEBPB/MITF/CEBPE/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/LBR/ACTN1/SH3PXD2A/FADD/BATF2/PIK3R1/CREBBP/CDK5RAP3/KAT8/VPS33A/ITPKB/MFHAS1/TESC/HIPK2/PRKDC/IKZF1/LEF1/ZFPM1
## GOBP_REGULATION_OF_HEMOPOIESIS                                                                     TGFBR2/ABL1/ZMIZ1/TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/STAT1/STAT3/IL34/PIK3R6/LRRC17/RASSF2/RNF41/ASH2L/P4HTM/ADA/EIF6/CD4/PRKCB/AGER/KMT2C/CDK6/SH3RF1/NFATC2/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/RARG/CBFB/TCF7/FAXDC2/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FBXO7/TESPA1/FADD/PIK3R1/CREBBP/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION                                                                                                                                                       TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/LRRC17/RASSF2/RNF41/ASH2L/P4HTM/EIF6/CD4/PRKCB/KMT2C/CDK6/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/RARG/CBFB/FAXDC2/CEBPB/MITF/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FADD/PIK3R1/CREBBP/ITPKB/TESC/PRKDC/LEF1/ZFPM1
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION                                                                                                                                                           TGFBR2/ABL1/ZMIZ1/TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/IL34/PIK3R6/LRRC17/RASSF2/RNF41/ADA/CD4/AGER/CDK6/SH3RF1/NFATC2/FOXP1/TRIB1/CBFB/TCF7/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/RB1/IL4/FBXO7/TESPA1/FADD/PIK3R1/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM                   KIF5C/ZMIZ1/KIDINS220/CUX1/ATN1/ZNF148/DYNC1H1/TREM2/PCNT/ANKRD11/TECR/ZC3H14/USP7/MFSD2A/RHOBTB2/HK1/WDR73/WWOX/RMND1/CLIP1/ZEB2/MED12L/PIGN/TRIM8/ASH1L/KANSL1/SPATA5/ADAR/EARS2/RNASEH2C/KMT2C/CCDC174/MED25/NFIA/IQSEC1/ARID1B/VPS53/ARNT2/POLR1C/COASY/DYRK1A/ADARB1/DAG1/RUSC2/IGF1R/KATNB1/RB1/TNIK/WDR81/HNMT/NEDD4L/RERE/TRAPPC9/LMAN2L/KAT8/UBE3B/B3GALNT2/ARID1A/AHDC1/GNAO1/CARS2/PRKDC/BICD2/DOCK8
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                                   ABL1/ZMIZ1/ATN1/TRIM27/SUFU/RALY/PARK7/WWOX/HDAC9/MED12L/TRIM8/TRERF1/URI1/PRKCB/MED13L/CBFA2T2/NCOR2/KMT2C/SIAH2/BRD4/SAP30L/CREG1/ZXDC/ARID1B/ACTN4/HDAC1/RYBP/SUPT3H/PHF12/TLE4/CBFB/MTA3/PARP9/RBPMS/SMARCC1/DYRK1A/LIMD1/ARID3A/RB1/LDB2/CDYL2/MAML1/MTA2/PXN/ACTN1/MED27/RERE/NCOA7/PDLIM1/FHL2/TADA2B/CREBBP/HDAC4/KAT8/EZH2/DMAP1/TLE3/ARID1A/NR0B2/ZNF653/LPIN1/TGFB1I1/HIPK2/ZFPM1
##                                                 Count
## GOBP_MYELOID_CELL_DIFFERENTIATION                  70
## GOBP_REGULATION_OF_HEMOPOIESIS                     62
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION    45
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION       45
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM               64
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY            64
em.C7 <- enricher(gene, TERM2GENE=m_C7, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 1909
em.C7.ge <- setReadable(em.C7, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C7.ge)
## [1] 1909    9
head(em.C7.ge)
##                                                                                                                                                                  ID
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                                                 GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                                                       GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                                                                         GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                                                           GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP
## GSE29618_BCELL_VS_MONOCYTE_DN                                                                                                         GSE29618_BCELL_VS_MONOCYTE_DN
##                                                                                                                                                         Description
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                                                 GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                                                       GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                                                                         GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                                                           GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP
## GSE29618_BCELL_VS_MONOCYTE_DN                                                                                                         GSE29618_BCELL_VS_MONOCYTE_DN
##                                                                                   GeneRatio
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                           44/1340
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP   42/1340
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                      42/1340
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                               37/1340
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                        39/1340
## GSE29618_BCELL_VS_MONOCYTE_DN                                                       39/1340
##                                                                                     BgRatio
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                         200/21341
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 197/21341
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                    200/21341
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                             175/21341
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                      197/21341
## GSE29618_BCELL_VS_MONOCYTE_DN                                                     200/21341
##                                                                                         pvalue
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                         1.803578e-13
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 1.933662e-12
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                    3.275419e-12
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                             5.147329e-11
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                      1.261579e-10
## GSE29618_BCELL_VS_MONOCYTE_DN                                                     2.019368e-10
##                                                                                       p.adjust
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                         9.182018e-10
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 4.922137e-09
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                    5.558385e-09
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                             6.551263e-08
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                      1.284540e-07
## GSE29618_BCELL_VS_MONOCYTE_DN                                                     1.468658e-07
##                                                                                         qvalue
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                         4.770940e-10
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 2.557522e-09
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                    2.888115e-09
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                             3.404010e-08
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                      6.674417e-08
## GSE29618_BCELL_VS_MONOCYTE_DN                                                     7.631086e-08
##                                                                                                                                                                                                                                                                                                                                                                            geneID
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                         NEDD9/RHBDF2/CHST11/PPP2R5C/GLIPR2/WDFY1/ADCY9/CCRL2/GPR68/ATP2A3/TRANK1/SYTL3/NR3C1/EPS15/GALM/MICAL2/PDE4B/PRKCE/CEP128/CMIP/OGDH/CBFA2T2/C1orf21/JOSD1/CLSTN3/AHNAK/ZNF532/PHF12/CAPN2/ARHGAP10/ADAM8/ANKRD27/TBXAS1/LRIG1/NCOA7/ABR/GABARAPL1/ST3GAL4/SNRNP200/SLCO3A1/GFPT2/FYN/GNAO1/KSR1
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP                 FKBP9/TGFBR2/SLC25A37/CELF2/PPP2R5C/F5/PTEN/TRANK1/WDFY2/ST3GAL2/ARSG/MICAL2/TRERF1/ZRANB1/MED13L/TBC1D1/SLMAP/ZDHHC18/MTURN/CAMK1D/RYBP/MTMR10/TLE4/RTN3/ARHGAP19/CAMP/RAB11FIP1/NFAM1/DGAT1/TBXAS1/CYTH1/RAP1GAP2/ACTN1/PTPRC/CLC/RAB37/MAN2A2/MTMR3/MAP3K1/BICD2/DOCK8/COTL1
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                                          TGFBR2/ZMIZ1/LRRFIP1/JARID2/RALB/PTEN/MTHFD2/CCL23/GNAQ/PACSIN2/SWAP70/TMEM156/SLC7A11/SRPK1/CHP1/CHST15/ALOX15/CREG1/PIK3CB/ACSL1/PTPRE/TRIB1/ARHGAP26/GSE1/ADAM8/NOTCH2/RNF24/TKT/PELI2/ACTN1/HK3/GABARAPL1/SELPLG/GFOD1/MCMBP/EPN2/RREB1/LIMK2/CMTM6/PTAFR/EHD1/ZBTB48
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                                                                                     WDFY4/XYLT1/CELF2/PPM1H/ADAM19/MYO18A/EXT1/ATP2A3/EML3/ACOX1/MICAL1/AMPD3/ABHD2/NFATC2/AHNAK/FOXK1/SPI1/TRIM26/RARG/DMXL1/ANXA6/PRKAB1/DYRK1A/NCK2/MAFK/MYO9B/RNF103/CRTC3/PIK3R5/ENTPD1/XPR1/SH3PXD2A/GALNT6/ARID1A/MTMR3/LPCAT2/TTC7A
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                                                                            ABL1/LPP/VDR/TPP1/TNS3/ETV6/EXT1/CLASP1/HMGXB4/STAT1/SPATS2L/BLVRA/KIAA1958/ZDHHC3/ADAR/NEK3/NCOR2/AGPAT1/MYLK/RYBP/MVB12A/CAPN2/GTPBP1/PARP9/CMTR1/PIK3AP1/RSAD2/XAF1/METRNL/TPM3/IFI27/RCC2/NCOA7/SASH1/DENND1A/GALNT6/MAN2A2/MGLL/KSR1
## GSE29618_BCELL_VS_MONOCYTE_DN                                                                                                       ZMIZ1/EPB41L3/SLC7A7/TPP1/SVIL/TPD52L2/EXT1/CALML4/GNAQ/NPL/BLVRA/CS/FKBP1A/RAB31/CHP1/CREG1/PLAUR/DENND5A/ACSL1/TRIB1/RAB20/RTN3/CAPN2/CD63/NOTCH2/SERINC5/CRISPLD2/TBXAS1/BEST1/PXN/ACTN1/PICALM/SELPLG/SLCO3A1/CTSB/PTAFR/DAPK1/FBP1/COTL1
##                                                                                   Count
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP                            44
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP    42
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP                                       42
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN                                                37
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP                                         39
## GSE29618_BCELL_VS_MONOCYTE_DN                                                        39
em.C8 <- enricher(gene, TERM2GENE=m_C8, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 77
em.C8.ge <- setReadable(em.C8, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C8.ge)
## [1] 77  9
head(em.C8.ge)
##                                                                                                                                    ID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                                                             TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                                                   LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB
## AIZARANI_LIVER_C20_LSECS_3                                                                                 AIZARANI_LIVER_C20_LSECS_3
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                                                       TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B       LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET
##                                                                                                                           Description
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                                                             TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                                                   LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB
## AIZARANI_LIVER_C20_LSECS_3                                                                                 AIZARANI_LIVER_C20_LSECS_3
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                                                       TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B       LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET
##                                                                    GeneRatio
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                                 53/1191
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                            36/1191
## AIZARANI_LIVER_C20_LSECS_3                                           50/1191
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                              47/1191
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B      25/1191
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET   41/1191
##                                                                      BgRatio
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                               276/18801
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                          169/18801
## AIZARANI_LIVER_C20_LSECS_3                                         295/18801
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                            270/18801
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B    103/18801
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 240/18801
##                                                                          pvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                               2.908945e-13
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                          9.244193e-11
## AIZARANI_LIVER_C20_LSECS_3                                         1.561487e-10
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                            2.204784e-10
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B    4.074602e-09
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 5.493455e-09
##                                                                        p.adjust
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                               1.646463e-10
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                          2.616107e-08
## AIZARANI_LIVER_C20_LSECS_3                                         2.946006e-08
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                            3.119769e-08
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B    4.612449e-07
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 5.182159e-07
##                                                                          qvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                               1.331991e-10
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                          2.116434e-08
## AIZARANI_LIVER_C20_LSECS_3                                         2.383323e-08
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                            2.523898e-08
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B    3.731477e-07
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 4.192374e-07
##                                                                                                                                                                                                                                                                                                                                                                                                           geneID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                               KIF13B/CPM/HSD17B12/RALB/STX3/ZNRF1/SMYD3/TMEM154/SWAP70/SYTL3/RHBDD2/PIK3R6/TMEM220/BLVRA/IL1RL1/EPAS1/GSTM3/CLU/SLC45A3/NENF/ALOX5AP/CD9/ARHGAP18/PHF20/FOXP1/GALC/KCNH2/NDST2/CD59/CD63/MITF/AKAP13/PRNP/TNIK/NDFIP2/TMOD1/CHN2/PARVB/PMP22/CTNNBL1/LAX1/TESPA1/SIGLEC8/ST3GAL4/IL5RA/SLC18A2/KIAA1522/ZBTB32/RAB37/TESC/CAPG/LPCAT2/ACOT7
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                                                                                                                             LPP/TNS3/ITPR2/SVIL/KIF13B/ETV6/LRRFIP1/CPM/LINC-PINT/RALGAPA2/SDCCAG8/EXT1/SPIDR/PLEKHA7/STK3/MECOM/ARHGAP24/CAMKMT/KIAA1958/PRKCE/AFF1/MED13L/OSBPL3/FOXP1/LAMB1/DOCK1/PFKFB3/PITPNC1/PCSK6/GALNT14/NCOA7/TRAPPC9/SASH1/TBC1D5/MSI2/MGLL
## AIZARANI_LIVER_C20_LSECS_3                                                                 DAAM1/SLC25A37/NID1/SPARC/APP/ANKRD11/TMEM51/ITPKC/ARHGEF7/COL4A1/ZEB2/CDC42BPB/FNDC3B/BAZ1A/ARSG/IL1RL1/AKAP12/TINAGL1/EPAS1/PTPN1/HERC1/FKBP1A/ASAP1/PLAUR/CD9/PLXNA2/NOTCH4/ARHGAP26/NOLC1/NDRG1/CD59/EFNB2/SSH1/PRICKLE2/SLC7A1/IFI27/ERG/LDB2/PXN/ACTN1/NCOA7/PDLIM1/SASH1/SOGA1/GRB10/ACP5/HIPK2/CDK17/ENG/SNX9
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                                                                               CUX1/SLC7A7/TPP1/TGFBI/HIPK3/TNFRSF1B/FCN1/UBXN11/GNAQ/SERF2/BACH1/ZEB2/SCPEP1/RASSF2/CD4/RAB31/CHST15/KCNE3/AHNAK/ACSL1/PRKAG2/PTPRE/HCK/SPI1/NACC2/RTN3/GAS7/TET3/EFHD2/CEBPB/RASSF3/NFAM1/NOTCH2/CRISPLD2/TKT/DICER1/RNF144B/USP15/CCNY/ENTPD1/SULF2/PICALM/NADK/HK2/CARS2/MAP3K1/COTL1
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B                                                                                                                                                                                      LPP/CELF2/KIF13B/RALGAPA2/SDCCAG8/WWOX/HERC1/PRKCE/KMT2C/ARHGAP18/DGKI/SEMA3C/OSBPL3/ARL15/FOXP1/MITF/CLNK/NEDD4L/NCOA7/PICALM/PTPRJ/TBC1D5/MSI2/MYRIP/GPHN
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET                                                                    SSH2/KIF13B/GPX3/LRRFIP1/LINC-PINT/TMEM51/EXT1/STAT3/SMYD3/MECOM/BACH1/UBE2D3/AAK1/HERC1/CSGALNACT1/PRKCE/ERC1/AFF1/MED13L/ABTB2/SH3RF1/AGBL4/IFRD1/AHNAK/SREBF2/PRKAG2/OSBPL3/ARID1B/ARL15/ACTN4/LAMB1/RBPMS/PFKFB3/DYRK1A/NDRG1/MCU/NEDD4L/NCOA7/SPTBN1/SLC25A25/MAP3K14
##                                                                    Count
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                                  53
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB                             36
## AIZARANI_LIVER_C20_LSECS_3                                            50
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL                               47
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B       25
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET    41
 # no gene set enrichment here using GSEA
em.H.gsea <- GSEA(geneList.na, TERM2GENE = m_H)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C2.gsea <- GSEA(geneList.na, TERM2GENE = m_C2)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C3.gsea <- GSEA(geneList.na, TERM2GENE = m_C3)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C5.gsea <- GSEA(geneList.na, TERM2GENE = m_C5)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C7.gsea <- GSEA(geneList.na, TERM2GENE = m_C7)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C8.gsea <- GSEA(geneList.na, TERM2GENE = m_C8)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
# Biological theme comparison
# to calculate enriched functional categories of each gene clusters
# Visualization of profile comparison
mydf <- data.frame(Entrez=names(geneList), FC=geneList)
colnames(mydf)[2] <- c("coeff")
mydf <- mydf[abs(mydf$coeff) > 0,]
mydf$Group <- "Hypermethylated"
mydf$Group[mydf$coeff < 0] <- "Hypomethylated"
table(mydf$Group)
## 
## Hypermethylated  Hypomethylated 
##             190            1319
mydf$Group <- as.factor(mydf$Group)
formula_res <- compareCluster(Entrez~Group, data=mydf, fun="enrichKEGG") # 10 
formula_res.ge <- setReadable(formula_res, 'org.Hs.eg.db', 'ENTREZID')
head(formula_res.ge)
##          Cluster          Group       ID
## 1 Hypomethylated Hypomethylated hsa04070
## 2 Hypomethylated Hypomethylated hsa00512
## 3 Hypomethylated Hypomethylated hsa04921
## 4 Hypomethylated Hypomethylated hsa05167
## 5 Hypomethylated Hypomethylated hsa04371
## 6 Hypomethylated Hypomethylated hsa04725
##                                       Description GeneRatio  BgRatio
## 1           Phosphatidylinositol signaling system    21/555  97/8113
## 2                Mucin type O-glycan biosynthesis    10/555  36/8113
## 3                      Oxytocin signaling pathway    24/555 154/8113
## 4 Kaposi sarcoma-associated herpesvirus infection    27/555 194/8113
## 5                        Apelin signaling pathway    21/555 139/8113
## 6                             Cholinergic synapse    18/555 113/8113
##         pvalue     p.adjust       qvalue
## 1 1.729020e-06 0.0005515573 0.0004313449
## 2 1.035595e-04 0.0120653439 0.0094356921
## 3 1.134672e-04 0.0120653439 0.0094356921
## 4 3.013938e-04 0.0240361524 0.0187974530
## 5 4.616639e-04 0.0294541565 0.0230345986
## 6 6.087850e-04 0.0323670716 0.0253126414
##                                                                                                                                                               geneID
## 1                               ITPKC/CALML4/PTEN/PI4KA/INPP5F/PIP4K2A/PIP5K1B/PRKCB/PI4KB/PIK3CB/DGKI/IP6K2/ITPK1/INPP5A/CALM1/DGKG/PIK3R1/ITPKB/INPP4A/ITPR1/MTMR3
## 2                                                                                   ST3GAL2/GALNT7/GALNTL6/GALNT12/GALNT10/GALNT16/ST6GALNAC4/GALNT14/ST3GAL1/GALNT6
## 3         CALML4/GNAQ/MYLK4/PIK3R6/KCNJ6/MAP2K5/CACNA2D1/PRKCB/CACNA1S/NFATC2/PRKAG2/CAMK1D/SRC/CACNA1D/MYLK/PRKAB1/PIK3R5/MYL9/CALM1/EEF2K/GNAO1/CAMK2G/ITPR1/MYLK3
## 4 CALML4/STAT1/STAT3/GNG7/TRAF3/PIK3R6/CDK6/MAPK13/ATG14/PIK3CB/GNG12/NFATC2/PREX1/HCK/SRC/TCF7/GNB5/ANGPT2/RB1/PIK3R5/CALM1/MAP1LC3B2/FADD/PIK3R1/CREBBP/ITPR1/LEF1
## 5                                   CALML4/GNG7/GNAQ/MYLK4/PIK3R6/PRKCE/GNG12/PRKAG2/MYLK/PRKAB1/GNB5/PIK3R5/JAG1/CALM1/MAP1LC3B2/MEF2D/HDAC4/SPHK2/ITPR1/CDH1/MYLK3
## 6                                                  GNG7/GNAQ/CREB3L2/PIK3R6/KCNJ6/CHRM1/PRKCB/CACNA1S/PIK3CB/GNG12/CACNA1D/GNB5/PIK3R5/PIK3R1/FYN/GNAO1/CAMK2G/ITPR1
##   Count
## 1    21
## 2    10
## 3    24
## 4    27
## 5    21
## 6    18
save(formula_res.ge, file=file.path(res.dir,
                paste0("compareCluster_enrichKEGG_CRA_CAMP_", timeStamp, ".RData")))

write.table(formula_res.ge,file=file.path(res.dir,
            paste0("compareCluster_enrichKEGG_CRA_CAMP_",timeStamp,".txt"))
            ,sep="\t",row.names=F,quote=F)

enrichplot::dotplot(formula_res.ge, x=~Group, showCategory=10)

pdf(file = file.path(sub.plots.dir, "dotplot_theme_cluster_hypo_enrichKEGG_CRA_CAMP.pdf"),
    width = 7, height = 7)
enrichplot::dotplot(formula_res.ge, x=~Group, showCategory=10)
dev.off()
## png 
##   2
# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
x2 <- pairwise_termsim(formula_res.ge)
emapplot(x2)

# if you don't want to plot effect sizes
#p1 <- cnetplot(edox, node_label="category") 
#p2 <- cnetplot(edox, node_label="gene") 
#p3 <- cnetplot(edox, node_label="all") 
#p4 <- cnetplot(edox, node_label="none") 

6. clusterProfileR enrichment analysis for CRA, CAMP and FHS

coeff.cra <- merge_CG.all$beta_coeff_cra
names(coeff.cra) <- merge_CG.all$Gene.x
coeff.cra.df <- data.frame(coeff.cra)
coeff.cra.df$Gene <- names(coeff.cra)
coeff.cra.uniq <- coeff.cra.df$Gene[!is.na(coeff.cra.df$Gene)]
coeff.cra.uniq <- coeff.cra.df[!is.na(coeff.cra.df$Gene), ]
coeff.cra.uniq <- coeff.cra.df[coeff.cra.df$Gene!="NA",]
coeff.cra.uniq <- coeff.cra.df[!duplicated(coeff.cra.df$Gene), ]

coeff.cra.uniq.v <- coeff.cra.uniq$coeff.cra
names(coeff.cra.uniq.v) <- coeff.cra.uniq$Gene
geneList <- coeff.cra.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')
## 'select()' returned 1:1 mapping between keys and columns
length(symbols.entrez) # 145
## [1] 145
#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 126
## [1] 126
ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)

# this looks interesting
edo.dgn <- enrichDGN(gene, pvalueCutoff = 0.05,pAdjustMethod = "BH",qvalueCutoff = 0.05)
barplot(edo.dgn, showCategory=20)

edo.dgn.ge <- setReadable(edo.dgn, 'org.Hs.eg.db', 'ENTREZID')
head(edo.dgn.ge)
##                ID                      Description GeneRatio   BgRatio
## C0861155 C0861155              Rhinoconjunctivitis     4/122  14/21671
## C0038273 C0038273    Stereotypic Movement Disorder     8/122 192/21671
## C0340076 C0340076 Asthmatic pulmonary eosinophilia     5/122  62/21671
## C0034068 C0034068           Pulmonary Eosinophilia     5/122  70/21671
## C0155877 C0155877                  Allergic asthma    10/122 371/21671
## C0035372 C0035372                    Rett Syndrome     8/122 234/21671
##                pvalue    p.adjust      qvalue
## C0861155 9.161390e-07 0.002841863 0.002411856
## C0038273 1.334676e-05 0.020700821 0.017568548
## C0340076 2.607175e-05 0.026958192 0.022879107
## C0034068 4.704474e-05 0.027615159 0.023436667
## C0155877 4.825106e-05 0.027615159 0.023436667
## C0035372 5.485541e-05 0.027615159 0.023436667
##                                                            geneID Count
## C0861155                                     IL13/IL4/IL5RA/NR0B2     4
## C0038273           EZR/SYNGAP1/IL13/TNIK/CREBBP/MITF/RERE/TRAPPC9     8
## C0340076                               IL13/SIGLEC8/IL4/IL5RA/EPX     5
## C0034068                               IL13/SIGLEC8/IL4/IL5RA/EPX     5
## C0155877 EZR/MCC/IL13/SIGLEC8/IL4/IL5RA/INPP4A/EPX/SLC25A25/ZFPM1    10
## C0035372             IGF1R/RHOBTB2/IL13/NCOR2/CREBBP/IL4/LBR/FBP1     8
# can be saved later depending on which view we choose
cnetplot(edo.dgn.ge, categorySize="qvalue", foldChange=geneList)

# without fold change but shows enriched terms, description and annotated genes, showCategory:number of enriched terms to display
cnetplot(edo.dgn.ge, node_label="all", categorySize="qvalue")

enrichplot::dotplot(edo.dgn.ge, showCategory=20) + ggtitle("dotplot for DO")
## wrong orderBy parameter; set to default `orderBy = "x"`

save(edo.dgn.ge, file=file.path(res.dir,
                paste0("enrich_DGN_CRA_CAMP_FHS_", timeStamp, ".RData")))

write.table(edo.dgn.ge@result,file=file.path(res.dir,
            paste0("enrichDGN_CRA_CAMP_FHS_",timeStamp,".txt"))
            ,sep="\t",row.names=F,quote=F)

pdf(file = file.path(sub.plots.dir, "barplot_enrichDGN_CRA_CAMP_FHS.pdf"),width = 7, height = 7)
barplot(edo.dgn.ge, showCategory=20)
dev.off()
## png 
##   2
pdf(file = file.path(sub.plots.dir, "dotplot_enrichDGN_CRA_CAMP_FHS.pdf"),width = 7, height = 7)
enrichplot::dotplot(edo.dgn.ge, showCategory=20) + ggtitle("dotplot for DO")
## wrong orderBy parameter; set to default `orderBy = "x"`
dev.off()
## png 
##   2
# no gene sets enriched here for diseases using DysGeNET
gse.dgn <- gseDGN(geneList,
              minGSSize     = 10,
              maxGSSize = 500,
              pvalueCutoff  = 0.05,
              pAdjustMethod = "BH",
              verbose       = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## no term enriched under specific pvalueCutoff...
#dgn <- setReadable(dgn, 'org.Hs.eg.db')
#head(dgn, 3)
#enrichplot::dotplot(gse.dgn, showCategory=30) + ggtitle("dotplot for DO")

# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
x <- pairwise_termsim(edo.dgn.ge)
emapplot(x)

pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_gseDGN_CRA_CAMP_FHS_overlap_genes.pdf"),
    width = 11, height = 9)
emapplot(x)
dev.off()
## png 
##   2
# nothing
enr.do <- enrichDO(gene = gene,
              ont           = "DO",
              pvalueCutoff  = 0.05,
              pAdjustMethod = "BH",
              universe      = univ,
              minGSSize     = 10,
              maxGSSize     = 500,
              qvalueCutoff  = 0.05,
              readable      = FALSE)
dim(enr.do) # nothing
## [1] 0 9
head(enr.do)
## [1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust   
## [7] qvalue      geneID      Count      
## <0 rows> (or 0-length row.names)
gene.df <- bitr(gene, fromType = "ENTREZID",
                 toType = c("ENSEMBL", "SYMBOL"),
                 OrgDb = org.Hs.eg.db)
## 'select()' returned 1:many mapping between keys and columns
## Warning in bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), :
## 1.59% of input gene IDs are fail to map...
head(gene.df)
##   ENTREZID         ENSEMBL  SYMBOL
## 1     3678 ENSG00000161638   ITGA5
## 3     9637 ENSG00000171055    FEZ2
## 4     2683 ENSG00000086062 B4GALT1
## 5      322 ENSG00000166313   APBB1
## 6      863 ENSG00000129993 CBFA2T3
## 7    23648 ENSG00000157216   SSBP3
# just returns functional profile of a geneset at a specific GO level not a P-value
ggo <- groupGO(gene     = gene,
                OrgDb    = org.Hs.eg.db,
                ont      = "BP",
                level    = 2,
                readable = TRUE)
dim(ggo)
## [1] 31  5
head(ggo)
##                    ID            Description Count GeneRatio
## GO:0000003 GO:0000003           reproduction     8     8/126
## GO:0002376 GO:0002376  immune system process    34    34/126
## GO:0006791 GO:0006791     sulfur utilization     0     0/126
## GO:0006794 GO:0006794 phosphorus utilization     0     0/126
## GO:0007610 GO:0007610               behavior     6     6/126
## GO:0008152 GO:0008152      metabolic process    92    92/126
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               geneID
## GO:0000003                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ITGA5/B4GALT1/NCOR2/SLC2A8/SLC19A1/FBXW8/MND1/CTSB
## GO:0002376                                                                                                                                                                                                                                                                                                                                                                                   ITGA5/B4GALT1/CBFA2T3/SSBP3/IGF1R/BANK1/PRKCH/EZR/SLC7A11/DOCK1/IL13/RASSF2/CAB39/HDAC1/SPI1/EVL/CREBBP/MITF/IL4/LBR/ELMO2/PRKCZ/SLC7A1/IL5RA/PRG2/EPX/TOLLIP/MFHAS1/TTC7A/GUSB/CTSB/DAPK2/MAD1L1/ZFPM1
## GO:0006791                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
## GO:0006794                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
## GO:0007610                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ITGA5/SYNGAP1/SLC7A11/PAK6/PRKCZ/GPR176
## GO:0008152 ITGA5/FEZ2/B4GALT1/APBB1/CBFA2T3/SSBP3/IGF1R/AXIN1/COL15A1/A2ML1/ELL2/ACOT7/UBE2QL1/SIK2/NDUFS6/MICAL2/BANK1/PRKCH/EZR/LTBP4/SYNGAP1/SLC7A11/UBE3B/IL13/RASSF2/KSR1/AGPAT1/NCOR2/PAK6/B4GALT7/CAB39/TFF1/SLC2A8/HDAC1/NOLC1/TMEM86B/SPI1/CLK3/CPSF4L/MCM2/SLC17A4/ST3GAL1/NHLRC4/ZNF862/ZNF662/ARID3A/USP20/TNIK/CREBBP/SLC19A1/MITF/DAP/IL4/LBR/NFIA/MECR/TRERF1/PNPLA1/PRKCZ/NDOR1/SEC16B/RERE/PTPRS/IL5RA/INPP4A/NR0B2/EPX/TOLLIP/PCYT1A/LPIN1/AQP1/GUCA2A/MFHAS1/TTC7A/NDFIP2/SLC25A25/FBP1/LPCAT3/FBXW8/GUSB/LRSAM1/MND1/TRAPPC9/ENG/LPCAT2/ACP5/CTSB/EZH2/SAMD11/MIR202/DAPK2/ZFPM1
# nothing came up here surprisingly for BP so chose ALL: BP, CC and MF
ego <- enrichGO(gene          = gene,
                OrgDb         = org.Hs.eg.db,
                ont           = "ALL",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.05,
                qvalueCutoff  = 0.05,
                readable      = TRUE)
dim(ego) # 8
## [1]  8 10
save(ego, file=file.path(res.dir,
                  paste0("enrich_GO_CRA_CAMP_FHS_all_overlap_results_", timeStamp, ".RData")))

write.table(ego@result,file=file.path(res.dir, 
       paste0("enrichGO_CRA_CAMP_FHS_all_overlap_results_",timeStamp,".txt"))
                ,sep="\t",row.names=F,quote=F)

head(ego@result, n=8)
##            ONTOLOGY         ID                                    Description
## GO:0045177       CC GO:0045177                            apical part of cell
## GO:0016324       CC GO:0016324                         apical plasma membrane
## GO:0031526       CC GO:0031526                          brush border membrane
## GO:0005903       CC GO:0005903                                   brush border
## GO:0001085       MF GO:0001085 RNA polymerase II transcription factor binding
## GO:0003714       MF GO:0003714             transcription corepressor activity
## GO:0004674       MF GO:0004674       protein serine/threonine kinase activity
## GO:0071617       MF GO:0071617      lysophospholipid acyltransferase activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0045177    10/115 433/19559 2.398922e-04 0.0268484867 0.0253711776
## GO:0016324     9/115 361/19559 2.838068e-04 0.0268484867 0.0253711776
## GO:0031526     4/115  58/19559 3.766855e-04 0.0268484867 0.0253711776
## GO:0005903     5/115 106/19559 4.067953e-04 0.0268484867 0.0253711776
## GO:0001085     6/119  56/18352 1.631659e-06 0.0006379785 0.0005736568
## GO:0003714     8/119 194/18352 3.888987e-05 0.0076029688 0.0068364291
## GO:0004674    11/119 435/18352 1.240552e-04 0.0161685331 0.0145384037
## GO:0071617     3/119  19/18352 2.387827e-04 0.0233410120 0.0209877454
##                                                                   geneID Count
## GO:0045177 AJAP1/EZR/SLC7A11/SLC17A4/TNIK/SLC19A1/PRKCZ/SLC7A1/AQP1/CTSB    10
## GO:0016324         AJAP1/EZR/SLC17A4/TNIK/SLC19A1/PRKCZ/SLC7A1/AQP1/CTSB     9
## GO:0031526                                  B4GALT1/SLC7A11/SLC19A1/AQP1     4
## GO:0005903                              B4GALT1/EZR/SLC7A11/SLC19A1/AQP1     5
## GO:0001085                             HDAC1/SPI1/CREBBP/RERE/FBP1/ZFPM1     6
## GO:0003714             CBFA2T3/NCOR2/HDAC1/CREBBP/TRERF1/RERE/NR0B2/EZH2     8
## GO:0004674    SIK2/PRKCH/LTBP4/KSR1/PAK6/CAB39/CLK3/TNIK/PRKCZ/ENG/DAPK2    11
## GO:0071617                                          AGPAT1/LPCAT3/LPCAT2     3
barplot(ego, showCategory=20)

enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")
## wrong orderBy parameter; set to default `orderBy = "x"`

# based on 1509 genes and 1390 unique genes
pdf(file = file.path(sub.plots.dir, "barplot_GOALL_CRA_CAMP_FHS_overlap_genes.pdf"),
    width = 7, height = 7)
barplot(ego, showCategory=20)
dev.off()
## png 
##   2
pdf(file = file.path(sub.plots.dir, "dotplot_GOALL_CRA_CAMP_FHS_overlap_genes.pdf"),
    width = 7, height = 7)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")
## wrong orderBy parameter; set to default `orderBy = "x"`
dev.off()
## png 
##   2
# not needed as readable=TRUE in enrichGO function
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)

p1 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)

# for CAMP
coeff.camp <- merge_CG.all$logFC
names(coeff.camp) <- merge_CG.all$Gene.x
coeff.camp.df <- data.frame(coeff.camp)
coeff.camp.df$Gene <- names(coeff.camp)
coeff.camp.uniq <- coeff.camp.df$Gene[!is.na(coeff.camp.df$Gene)]
coeff.camp.uniq <- coeff.camp.df[!is.na(coeff.camp.df$Gene), ]
coeff.camp.uniq <- coeff.camp.df[coeff.camp.df$Gene!="NA",]
coeff.camp.uniq <- coeff.camp.df[!duplicated(coeff.camp.df$Gene), ]

coeff.camp.uniq.v <- coeff.camp.uniq$coeff.camp
names(coeff.camp.uniq.v) <- coeff.camp.uniq$Gene
geneList <- coeff.camp.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')
## 'select()' returned 1:1 mapping between keys and columns
length(symbols.entrez) # 145
## [1] 145
#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 126
## [1] 126
ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)

ego <- enrichGO(gene          = gene,
                OrgDb         = org.Hs.eg.db,
                ont           = "ALL",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.05,
                qvalueCutoff  = 0.05,
                readable      = TRUE)

# would be same outcome as for CRA as the gene list is same, just the effect estimates would change if we plot those
dim(ego)
## [1]  8 10
head(ego@result)
##            ONTOLOGY         ID                                    Description
## GO:0045177       CC GO:0045177                            apical part of cell
## GO:0016324       CC GO:0016324                         apical plasma membrane
## GO:0031526       CC GO:0031526                          brush border membrane
## GO:0005903       CC GO:0005903                                   brush border
## GO:0001085       MF GO:0001085 RNA polymerase II transcription factor binding
## GO:0003714       MF GO:0003714             transcription corepressor activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0045177    10/115 433/19559 2.398922e-04 0.0268484867 0.0253711776
## GO:0016324     9/115 361/19559 2.838068e-04 0.0268484867 0.0253711776
## GO:0031526     4/115  58/19559 3.766855e-04 0.0268484867 0.0253711776
## GO:0005903     5/115 106/19559 4.067953e-04 0.0268484867 0.0253711776
## GO:0001085     6/119  56/18352 1.631659e-06 0.0006379785 0.0005736568
## GO:0003714     8/119 194/18352 3.888987e-05 0.0076029688 0.0068364291
##                                                                   geneID Count
## GO:0045177 EZR/SLC7A11/AJAP1/SLC17A4/SLC7A1/TNIK/PRKCZ/SLC19A1/AQP1/CTSB    10
## GO:0016324         EZR/AJAP1/SLC17A4/SLC7A1/TNIK/PRKCZ/SLC19A1/AQP1/CTSB     9
## GO:0031526                                  B4GALT1/SLC7A11/SLC19A1/AQP1     4
## GO:0005903                              B4GALT1/EZR/SLC7A11/SLC19A1/AQP1     5
## GO:0001085                             SPI1/HDAC1/CREBBP/RERE/FBP1/ZFPM1     6
## GO:0003714             CBFA2T3/NCOR2/HDAC1/TRERF1/CREBBP/RERE/EZH2/NR0B2     8
barplot(ego, showCategory=20)

#dotplot(ego)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")
## wrong orderBy parameter; set to default `orderBy = "x"`

#gseaplot(y, y[1,1], title=y[1,2])

# not needed here as readable was TRUE in the enrichGO function
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)

p2 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)

# only with CRA (a) and CAMP (b); for better visualizing chose nrow=2
cowplot::plot_grid(p1, p2, ncol=1,nrow=2, labels=LETTERS[1:2], rel_widths=c(.8, .8))

# For FHS
coeff.fhs <- merge_CG.all$IgE.Estimate
names(coeff.fhs) <- merge_CG.all$Gene.x
coeff.fhs.df <- data.frame(coeff.fhs)
coeff.fhs.df$Gene <- names(coeff.fhs)
coeff.fhs.uniq <- coeff.fhs.df$Gene[!is.na(coeff.fhs.df$Gene)]
coeff.fhs.uniq <- coeff.fhs.df[!is.na(coeff.fhs.df$Gene), ]
coeff.fhs.uniq <- coeff.fhs.df[coeff.fhs.df$Gene!="NA",]
coeff.fhs.uniq <- coeff.fhs.df[!duplicated(coeff.fhs.df$Gene), ]

coeff.fhs.uniq.v <- coeff.fhs.uniq$coeff.fhs
names(coeff.fhs.uniq.v) <- coeff.fhs.uniq$Gene
geneList <- coeff.fhs.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')
## 'select()' returned 1:1 mapping between keys and columns
length(symbols.entrez) # 145
## [1] 145
#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 126
## [1] 126
ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)

ego <- enrichGO(gene          = gene,
                OrgDb         = org.Hs.eg.db,
                ont           = "ALL",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.05,
                qvalueCutoff  = 0.05,
                readable      = TRUE)
dim(ego)
## [1]  8 10
head(ego@result)
##            ONTOLOGY         ID                                    Description
## GO:0045177       CC GO:0045177                            apical part of cell
## GO:0016324       CC GO:0016324                         apical plasma membrane
## GO:0031526       CC GO:0031526                          brush border membrane
## GO:0005903       CC GO:0005903                                   brush border
## GO:0001085       MF GO:0001085 RNA polymerase II transcription factor binding
## GO:0003714       MF GO:0003714             transcription corepressor activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0045177    10/115 433/19559 2.398922e-04 0.0268484867 0.0253711776
## GO:0016324     9/115 361/19559 2.838068e-04 0.0268484867 0.0253711776
## GO:0031526     4/115  58/19559 3.766855e-04 0.0268484867 0.0253711776
## GO:0005903     5/115 106/19559 4.067953e-04 0.0268484867 0.0253711776
## GO:0001085     6/119  56/18352 1.631659e-06 0.0006379785 0.0005736568
## GO:0003714     8/119 194/18352 3.888987e-05 0.0076029688 0.0068364291
##                                                                   geneID Count
## GO:0045177 AQP1/SLC19A1/EZR/SLC17A4/AJAP1/CTSB/TNIK/SLC7A11/PRKCZ/SLC7A1    10
## GO:0016324         AQP1/SLC19A1/EZR/SLC17A4/AJAP1/CTSB/TNIK/PRKCZ/SLC7A1     9
## GO:0031526                                  B4GALT1/AQP1/SLC19A1/SLC7A11     4
## GO:0005903                              B4GALT1/AQP1/SLC19A1/EZR/SLC7A11     5
## GO:0001085                             SPI1/CREBBP/HDAC1/RERE/FBP1/ZFPM1     6
## GO:0003714             CBFA2T3/NCOR2/CREBBP/HDAC1/RERE/EZH2/NR0B2/TRERF1     8
barplot(ego, showCategory=20)

#dotplot(ego)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")
## wrong orderBy parameter; set to default `orderBy = "x"`

#gseaplot(y, y[1,1], title=y[1,2])

#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)

p3 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)

pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_coeff_overlap_with_FHS_univ.pdf"),
    width = 22, height = 9)
# Genes and gene ontology enrichments network
cowplot::plot_grid(p1, p2,ncol=2, labels=LETTERS[1:2], rel_widths=c(.8, .8))
dev.off()
## png 
##   2
# for ease in visualizing
cowplot::plot_grid(p1, p2, p3, ncol=1, nrow=3, labels=LETTERS[1:3], rel_widths=c(.8, .8,.8))

pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_FHS_coeff_overlap_univ.pdf"),
    width = 35, height = 9)
# Genes and gene ontology enrichments network
cowplot::plot_grid(p1, p2, p3, ncol=3, nrow=1, labels=LETTERS[1:3], rel_widths=c(.8, .8,.8))
dev.off()
## png 
##   2
# If you don't want effect estimates
cnetplot(ego, categorySize="qvalue", node_label="all")

# save it
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_FHS_overlap_without_coeff.pdf"),
    width = 11, height = 9)
cnetplot(ego, categorySize="qvalue", node_label="all")
dev.off()
## png 
##   2
# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
# The plot would look same for CRA, CAMP and FHS as you are only plotting pvalues and terms
x1 <- pairwise_termsim(ego)
emapplot(x1)

pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_enrichGO_CRA_CAMP_FHS_overlap_genes.pdf"),
    width = 11, height = 9)
emapplot(x1)
dev.off()
## png 
##   2
kk <- enrichKEGG(gene         = gene,
                 organism     = 'hsa',
                 pvalueCutoff = 0.05,
                 pAdjustMethod = "BH",
                 qvalueCutoff = 0.05,
                 minGSSize = 50,
                 maxGSSize = 500)
dim(kk) # nothing
## [1] 0 9
kk.ge <- setReadable(kk, 'org.Hs.eg.db', 'ENTREZID')
head(kk.ge)
## [1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust   
## [7] qvalue      geneID      Count      
## <0 rows> (or 0-length row.names)
#save(kk.ge, file=file.path(res.dir,
#                  paste0("enrich_Kegg_CRA_CAMP_FHS_genomewide_thresh_", timeStamp, #".RData")))

#write.table(kk.ge@result,file=file.path(res.dir, 
#       paste0("enrichKegg_CRA_CAMP_gw_thresh_",timeStamp,".txt"))
#                ,sep="\t",row.names=F,quote=F)

geneList.na <- geneList[names(geneList)!="NA"]
kk2 <- gseKEGG(geneList     = geneList.na,
               organism     = 'hsa',
               minGSSize    = 50,
               pvalueCutoff = 0.05,
               pAdjustMethod = "BH",
               maxGSSize = 500,
               by = "fgsea",
               verbose      = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
head(kk2)
## [1] ID              Description     setSize         enrichmentScore
## [5] NES             pvalue          p.adjust        qvalues        
## <0 rows> (or 0-length row.names)
#preparing geneSet collections...
#GSEA analysis...
#no term enriched under specific pvalueCutoff...

# GSEA , no enrichment
ego.gse <- gseGO(geneList     = geneList.na,
              OrgDb        = org.Hs.eg.db,
              ont          = "BP",
              minGSSize    = 50,
              maxGSSize    = 500,
              pvalueCutoff = 0.05,
              pAdjustMethod = "BH",
              verbose      = TRUE)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
dim(ego.gse)
## [1] 0 8
# H and C2,3,5,7,8
# Gene set enrichment analysis.. The same pulled gene sets from msigdbr could be used as above in section 4

# enrichments
em.H <- enricher(gene, TERM2GENE=m_H, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # none, nothing was sig
dim(em.H)
## [1] 0 9
em.C2 <- enricher(gene, TERM2GENE=m_C2, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 34
em.C2.ge <- setReadable(em.C2, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C2.ge)
## [1] 34  9
# top curated gene set is for KEGG asthma which was interesting
head(em.C2.ge)
##                                                        ID
## KEGG_ASTHMA                                   KEGG_ASTHMA
## SENESE_HDAC3_TARGETS_UP           SENESE_HDAC3_TARGETS_UP
## PID_ERA_GENOMIC_PATHWAY           PID_ERA_GENOMIC_PATHWAY
## APPEL_IMATINIB_RESPONSE           APPEL_IMATINIB_RESPONSE
## PEREZ_TP63_TARGETS                     PEREZ_TP63_TARGETS
## WEST_ADRENOCORTICAL_TUMOR_UP WEST_ADRENOCORTICAL_TUMOR_UP
##                                               Description GeneRatio   BgRatio
## KEGG_ASTHMA                                   KEGG_ASTHMA     4/123  30/21697
## SENESE_HDAC3_TARGETS_UP           SENESE_HDAC3_TARGETS_UP    12/123 496/21697
## PID_ERA_GENOMIC_PATHWAY           PID_ERA_GENOMIC_PATHWAY     5/123  64/21697
## APPEL_IMATINIB_RESPONSE           APPEL_IMATINIB_RESPONSE     4/123  33/21697
## PEREZ_TP63_TARGETS                     PEREZ_TP63_TARGETS    10/123 360/21697
## WEST_ADRENOCORTICAL_TUMOR_UP WEST_ADRENOCORTICAL_TUMOR_UP     9/123 298/21697
##                                    pvalue   p.adjust     qvalue
## KEGG_ASTHMA                  2.404427e-05 0.01667970 0.01476813
## SENESE_HDAC3_TARGETS_UP      2.580739e-05 0.01667970 0.01476813
## PID_ERA_GENOMIC_PATHWAY      3.148396e-05 0.01667970 0.01476813
## APPEL_IMATINIB_RESPONSE      3.543317e-05 0.01667970 0.01476813
## PEREZ_TP63_TARGETS           3.978936e-05 0.01667970 0.01476813
## WEST_ADRENOCORTICAL_TUMOR_UP 5.164913e-05 0.01804276 0.01597498
##                                                                                                    geneID
## KEGG_ASTHMA                                                                             PRG2/IL4/IL13/EPX
## SENESE_HDAC3_TARGETS_UP      B4GALT1/GPR176/UBE2QL1/EZR/MICAL2/CTSB/LPIN1/BICD2/PMP22/TNIK/SLC7A11/SLC7A1
## PID_ERA_GENOMIC_PATHWAY                                                      APBB1/NCOR2/HDAC1/TFF1/NR0B2
## APPEL_IMATINIB_RESPONSE                                                                GUSB/ENG/ACP5/CTSB
## PEREZ_TP63_TARGETS                     KCNH2/PAK6/UBE2QL1/METRNL/IGF1R/RAB11FIP4/PRKCH/ST3GAL1/KSR1/ZFPM1
## WEST_ADRENOCORTICAL_TUMOR_UP                       ELMO2/ACOT7/MCM2/HDAC1/EZH2/LPIN1/BICD2/MAD1L1/SLC7A11
##                              Count
## KEGG_ASTHMA                      4
## SENESE_HDAC3_TARGETS_UP         12
## PID_ERA_GENOMIC_PATHWAY          5
## APPEL_IMATINIB_RESPONSE          4
## PEREZ_TP63_TARGETS              10
## WEST_ADRENOCORTICAL_TUMOR_UP     9
# regulatory target/motif gene sets
em.C3 <- enricher(gene, TERM2GENE=m_C3, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 1
em.C3.ge <- setReadable(em.C3, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C3.ge)
## [1] 1 9
head(em.C3.ge)
##                ID Description GeneRatio   BgRatio       pvalue    p.adjust
## GATA1_05 GATA1_05    GATA1_05     9/123 284/28103 4.663766e-06 0.008865819
##             qvalue                                                   geneID
## GATA1_05 0.0075553 GUCA2A/PRG2/IL4/SAMD11/TMEM86B/SLC25A25/SEC16B/EPX/ZFPM1
##          Count
## GATA1_05     9
# ontology gene sets
em.C5 <- enricher(gene, TERM2GENE=m_C5, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 4
em.C5.ge <- setReadable(em.C5, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C5.ge)
## [1] 4 9
head(em.C5.ge)
##                                                                                                      ID
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY                         GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                         GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
## GOBP_GRANULOCYTE_DIFFERENTIATION                                       GOBP_GRANULOCYTE_DIFFERENTIATION
##                                                                                             Description
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY                         GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                         GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
## GOBP_GRANULOCYTE_DIFFERENTIATION                                       GOBP_GRANULOCYTE_DIFFERENTIATION
##                                                     GeneRatio   BgRatio
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING     6/121  52/19303
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY                 9/121 182/19303
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                12/121 480/19303
## GOBP_GRANULOCYTE_DIFFERENTIATION                        4/121  33/19303
##                                                           pvalue    p.adjust
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING 8.614132e-07 0.003211349
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY             2.204261e-06 0.004108742
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY             4.909021e-05 0.048673240
## GOBP_GRANULOCYTE_DIFFERENTIATION                    5.222451e-05 0.048673240
##                                                          qvalue
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING 0.002907043
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY             0.003719400
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY             0.044060992
## GOBP_GRANULOCYTE_DIFFERENTIATION                    0.044060992
##                                                                                                                         geneID
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING                                          SPI1/CREBBP/HDAC1/RERE/FBP1/ZFPM1
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY                                CBFA2T3/NCOR2/CREBBP/HDAC1/RERE/EZH2/NR0B2/TRERF1/ZFPM1
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY             CBFA2T3/APBB1/NCOR2/CREBBP/HDAC1/RERE/EZH2/NR0B2/LPIN1/TRERF1/ARID3A/ZFPM1
## GOBP_GRANULOCYTE_DIFFERENTIATION                                                                        CBFA2T3/LBR/SPI1/ZFPM1
##                                                     Count
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING     6
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY                 9
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY                12
## GOBP_GRANULOCYTE_DIFFERENTIATION                        4
# immunologic signature gene sets
em.C7 <- enricher(gene, TERM2GENE=m_C7, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 28
em.C7.ge <- setReadable(em.C7, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C7.ge)
## [1] 28  9
head(em.C7.ge)
##                                                                                                                                      ID
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN                   GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN                     GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP                         GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                                                 GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                                                             GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP
##                                                                                                                             Description
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN                   GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN                     GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP                         GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                                                 GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                                                             GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP
##                                                                     GeneRatio
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN              8/123
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP     7/123
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN               7/123
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP                 8/123
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                     8/123
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                                   8/123
##                                                                       BgRatio
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN          178/21341
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 134/21341
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN           139/21341
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP             196/21341
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                 198/21341
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                               200/21341
##                                                                           pvalue
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN          9.114129e-06
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 1.274884e-05
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN           1.618327e-05
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP             1.834254e-05
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                 1.973432e-05
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                               2.121375e-05
##                                                                       p.adjust
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN          0.01082697
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 0.01082697
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN           0.01082697
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP             0.01082697
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                 0.01082697
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                               0.01082697
##                                                                          qvalue
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN          0.009699708
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 0.009699708
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN           0.009699708
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP             0.009699708
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                 0.009699708
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                               0.009699708
##                                                                                                                 geneID
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN          MPRIP/ELMO2/SLC45A4/NCOR2/GUSB/PCYT1A/MICAL2/PRKCH
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP  B4GALT1/NCOR2/NDOR1/MIR202/TMEM86B/RHOBTB2/TOMM34
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN                     ITGA5/LRIG1/RERE/IGF1R/EVL/MAD1L1/MFHAS1
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP             LPCAT2/ENG/MICAL2/FBP1/ZNF862/ST3GAL1/IL5RA/MFHAS1
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                       MPRIP/LRIG1/LPIN1/PRKCH/LTBP4/EVL/TNIK/PRKCZ
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                                       PTPRS/DAP/EZR/EZH2/ENG/ACP5/ST3GAL1/MFHAS1
##                                                                     Count
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN              8
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP     7
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN               7
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP                 8
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP                                     8
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP                                   8
# cell type signature gene sets
em.C8 <- enricher(gene, TERM2GENE=m_C8, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 2
em.C8.ge <- setReadable(em.C8, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C8.ge)
## [1] 2 9
head(em.C8.ge)
##                                                                                                                    ID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                                             TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2
##                                                                                                           Description
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                                             TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2
##                                                            GeneRatio   BgRatio
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                           9/112 276/18801
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2     5/112  97/18801
##                                                                  pvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                       4.084318e-05
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 2.858505e-04
##                                                              p.adjust    qvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                       0.01311066 0.0119950
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 0.04587901 0.0419749
##                                                                                                             geneID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                       ACOT7/KCNH2/MITF/SIGLEC8/LPCAT2/IL5RA/PMP22/TNIK/NDFIP2
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2                            AQP1/TMEM86B/ACP5/NR0B2/FBP1
##                                                            Count
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL                           9
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2     5
 # no gene set enrichment using GSEA
em.H.gsea <- GSEA(geneList.na, TERM2GENE = m_H)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C2.gsea <- GSEA(geneList.na, TERM2GENE = m_C2)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C3.gsea <- GSEA(geneList.na, TERM2GENE = m_C3)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C5.gsea <- GSEA(geneList.na, TERM2GENE = m_C5)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C7.gsea <- GSEA(geneList.na, TERM2GENE = m_C7)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
em.C8.gsea <- GSEA(geneList.na, TERM2GENE = m_C8)
## preparing geneSet collections...
## GSEA analysis...
## no term enriched under specific pvalueCutoff...
# Biological theme comparison
# to calculate enriched functional categories of each gene clusters
# Visualization of profile comparison
mydf <- data.frame(Entrez=names(geneList), FC=geneList)
colnames(mydf)[2] <- c("coeff")
mydf <- mydf[abs(mydf$coeff) > 0,]
mydf$Group <- "Hypermethylated"
mydf$Group[mydf$coeff < 0] <- "Hypomethylated"
table(mydf$Group)
## 
## Hypermethylated  Hypomethylated 
##               6             139
mydf$Group <- as.factor(mydf$Group)
formula_res <- compareCluster(Entrez~Group, data=mydf, fun="enrichKEGG") 
formula_res.ge <- setReadable(formula_res, 'org.Hs.eg.db', 'ENTREZID')
head(formula_res.ge)
##          Cluster          Group       ID Description GeneRatio BgRatio
## 1 Hypomethylated Hypomethylated hsa05310      Asthma      4/63 31/8113
##         pvalue   p.adjust     qvalue            geneID Count
## 1 8.877957e-05 0.01455985 0.01455985 PRG2/IL4/IL13/EPX     4
enrichplot::dotplot(formula_res.ge, x=~Group, showCategory=10)

x2 <- pairwise_termsim(formula_res.ge)
#enrichplot::emapplot(x2)
# if you don't want to plot effect sizes
#p1 <- cnetplot(edox, node_label="category") 
#p2 <- cnetplot(edox, node_label="gene") 
#p3 <- cnetplot(edox, node_label="all") 
#p4 <- cnetplot(edox, node_label="none") 

save(formula_res.ge, file=file.path(res.dir,
                paste0("compareCluster_enrichKEGG_CRA_CAMP_FHS_", timeStamp, ".RData")))

write.table(formula_res.ge,file=file.path(res.dir,
            paste0("compareCluster_enrichKEGG_CRA_CAMP_FHS_",timeStamp,".txt"))
            ,sep="\t",row.names=F,quote=F)

#Test for over-representation (enrichment), small probability of # seeing an equal or bigger overlap
# Hypergeometric pvalue for the overlap of all 3 cohorts

# 193 is the total overlap between CRA, CAMP and FHS
# 10426 is the overlap of significant DM CpGs in CRA and CAMP because eventually this number is checked for overlap with FHS
# 406318 is the platform overlap between 450K of FHS and EPIC for CRA and CAMP so the background that was tested for the analysis
# 490 is the significant DM CpGs in FHS
# we discussed removing 51 sites that did not exist on both platforms
phyper(193-1, 10426, 406318-10426, 490-51, lower.tail = FALSE, log.p=F)
## [1] 7.22766e-182
#7.22766e-182

# reference: https://seqqc.wordpress.com/2019/07/25/how-to-use-phyper-in-r/
# phyper(Overlap-1, group2, Total-group2, group1,lower.tail= FALSE)

# also this works:
# fisher.test(matrix(c(Overlap, group2-Overlap, group1-Overlap, Total-group2-group1 +Overlap), 2, 2), alternative='greater')$p.value
# fisher.test(matrix(c(193, 10426-193, 439-193, 406318-10426-439+193), 2, 2), alternative='greater')$p.value

7. Session info

print(Sys.Date())
## [1] "2021-11-29"
print(Sys.time())
## [1] "2021-11-29 21:36:07 EST"
sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS:   /app/R-4.0.3@i86-rhel7.0/lib64/R/lib/libRblas.so
## LAPACK: /app/R-4.0.3@i86-rhel7.0/lib64/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] pathview_1.30.1             msigdbr_7.4.1              
##  [3] magrittr_2.0.1              ggnewscale_0.4.5           
##  [5] lattice_0.20-45             gridExtra_2.3              
##  [7] gprofiler2_0.2.1            knitr_1.36                 
##  [9] R.utils_2.11.0              R.oo_1.24.0                
## [11] R.methodsS3_1.8.1           org.Hs.eg.db_3.12.0        
## [13] AnnotationDbi_1.52.0        clusterProfiler_3.18.1     
## [15] enrichplot_1.10.2           DOSE_3.16.0                
## [17] QQperm_1.0.1                gplots_3.1.1               
## [19] gProfileR_0.7.0             DMRcate_2.4.1              
## [21] ggpubr_0.4.0                ggplot2_3.3.5              
## [23] minfi_1.36.0                bumphunter_1.32.0          
## [25] locfit_1.5-9.4              iterators_1.0.13           
## [27] foreach_1.5.1               Biostrings_2.58.0          
## [29] XVector_0.30.0              SummarizedExperiment_1.20.0
## [31] Biobase_2.50.0              MatrixGenerics_1.2.1       
## [33] matrixStats_0.61.0          GenomicRanges_1.42.0       
## [35] GenomeInfoDb_1.26.7         IRanges_2.24.1             
## [37] S4Vectors_0.28.1            BiocGenerics_0.36.1        
## [39] limma_3.46.0               
## 
## loaded via a namespace (and not attached):
##   [1] rappdirs_0.3.3                                     
##   [2] rtracklayer_1.50.0                                 
##   [3] ragg_1.1.3                                         
##   [4] tidyr_1.1.4                                        
##   [5] bit64_4.0.5                                        
##   [6] DelayedArray_0.16.3                                
##   [7] data.table_1.14.2                                  
##   [8] rpart_4.1-15                                       
##   [9] KEGGREST_1.30.1                                    
##  [10] RCurl_1.98-1.5                                     
##  [11] GEOquery_2.58.0                                    
##  [12] AnnotationFilter_1.14.0                            
##  [13] generics_0.1.1                                     
##  [14] GenomicFeatures_1.42.3                             
##  [15] preprocessCore_1.52.1                              
##  [16] cowplot_1.1.1                                      
##  [17] RSQLite_2.2.8                                      
##  [18] shadowtext_0.0.9                                   
##  [19] bit_4.0.4                                          
##  [20] tzdb_0.2.0                                         
##  [21] xml2_1.3.2                                         
##  [22] httpuv_1.6.3                                       
##  [23] assertthat_0.2.1                                   
##  [24] viridis_0.6.2                                      
##  [25] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
##  [26] xfun_0.26                                          
##  [27] hms_1.1.1                                          
##  [28] jquerylib_0.1.4                                    
##  [29] babelgene_21.4                                     
##  [30] evaluate_0.14                                      
##  [31] missMethyl_1.24.0                                  
##  [32] promises_1.2.0.1                                   
##  [33] fansi_0.5.0                                        
##  [34] scrime_1.3.5                                       
##  [35] progress_1.2.2                                     
##  [36] caTools_1.18.2                                     
##  [37] dbplyr_2.1.1                                       
##  [38] readxl_1.3.1                                       
##  [39] Rgraphviz_2.34.0                                   
##  [40] igraph_1.2.6                                       
##  [41] DBI_1.1.1                                          
##  [42] htmlwidgets_1.5.4                                  
##  [43] reshape_0.8.8                                      
##  [44] purrr_0.3.4                                        
##  [45] ellipsis_0.3.2                                     
##  [46] crosstalk_1.2.0                                    
##  [47] dplyr_1.0.7                                        
##  [48] backports_1.3.0                                    
##  [49] permute_0.9-5                                      
##  [50] annotate_1.68.0                                    
##  [51] biomaRt_2.46.3                                     
##  [52] sparseMatrixStats_1.2.1                            
##  [53] vctrs_0.3.8                                        
##  [54] ensembldb_2.14.1                                   
##  [55] abind_1.4-5                                        
##  [56] cachem_1.0.6                                       
##  [57] withr_2.4.2                                        
##  [58] ggforce_0.3.3                                      
##  [59] Gviz_1.34.1                                        
##  [60] BSgenome_1.58.0                                    
##  [61] checkmate_2.0.0                                    
##  [62] GenomicAlignments_1.26.0                           
##  [63] prettyunits_1.1.1                                  
##  [64] mclust_5.4.7                                       
##  [65] cluster_2.1.2                                      
##  [66] ExperimentHub_1.16.1                               
##  [67] lazyeval_0.2.2                                     
##  [68] crayon_1.4.2                                       
##  [69] genefilter_1.72.1                                  
##  [70] labeling_0.4.2                                     
##  [71] edgeR_3.32.1                                       
##  [72] pkgconfig_2.0.3                                    
##  [73] tweenr_1.0.2                                       
##  [74] nlme_3.1-153                                       
##  [75] ProtGenerics_1.22.0                                
##  [76] nnet_7.3-16                                        
##  [77] rlang_0.4.11                                       
##  [78] lifecycle_1.0.1                                    
##  [79] downloader_0.4                                     
##  [80] BiocFileCache_1.14.0                               
##  [81] AnnotationHub_2.22.1                               
##  [82] dichromat_2.0-0                                    
##  [83] polyclip_1.10-0                                    
##  [84] cellranger_1.1.0                                   
##  [85] graph_1.68.0                                       
##  [86] rngtools_1.5.2                                     
##  [87] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
##  [88] base64_2.0                                         
##  [89] Matrix_1.3-4                                       
##  [90] carData_3.0-4                                      
##  [91] Rhdf5lib_1.12.1                                    
##  [92] base64enc_0.1-3                                    
##  [93] viridisLite_0.4.0                                  
##  [94] png_0.1-7                                          
##  [95] bitops_1.0-7                                       
##  [96] KernSmooth_2.23-20                                 
##  [97] rhdf5filters_1.2.1                                 
##  [98] blob_1.2.2                                         
##  [99] DelayedMatrixStats_1.12.3                          
## [100] doRNG_1.8.2                                        
## [101] qvalue_2.22.0                                      
## [102] stringr_1.4.0                                      
## [103] nor1mix_1.3-0                                      
## [104] readr_2.0.2                                        
## [105] jpeg_0.1-9                                         
## [106] rstatix_0.7.0                                      
## [107] ggsignif_0.6.3                                     
## [108] scales_1.1.1                                       
## [109] memoise_2.0.0                                      
## [110] plyr_1.8.6                                         
## [111] zlibbioc_1.36.0                                    
## [112] scatterpie_0.1.7                                   
## [113] compiler_4.0.3                                     
## [114] RColorBrewer_1.1-2                                 
## [115] illuminaio_0.32.0                                  
## [116] KEGGgraph_1.50.0                                   
## [117] Rsamtools_2.6.0                                    
## [118] DSS_2.38.0                                         
## [119] htmlTable_2.2.1                                    
## [120] Formula_1.2-4                                      
## [121] MASS_7.3-54                                        
## [122] tidyselect_1.1.1                                   
## [123] stringi_1.7.5                                      
## [124] forcats_0.5.1                                      
## [125] textshaping_0.3.3                                  
## [126] highr_0.9                                          
## [127] yaml_2.2.1                                         
## [128] GOSemSim_2.16.1                                    
## [129] askpass_1.1                                        
## [130] ggrepel_0.9.1                                      
## [131] latticeExtra_0.6-29                                
## [132] sass_0.4.0                                         
## [133] VariantAnnotation_1.36.0                           
## [134] fastmatch_1.1-3                                    
## [135] tools_4.0.3                                        
## [136] rio_0.5.27                                         
## [137] rstudioapi_0.13                                    
## [138] foreign_0.8-81                                     
## [139] bsseq_1.26.0                                       
## [140] farver_2.1.0                                       
## [141] ggraph_2.0.5                                       
## [142] rvcheck_0.1.8                                      
## [143] digest_0.6.28                                      
## [144] BiocManager_1.30.16                                
## [145] shiny_1.7.0                                        
## [146] quadprog_1.5-8                                     
## [147] Rcpp_1.0.7                                         
## [148] car_3.0-11                                         
## [149] siggenes_1.64.0                                    
## [150] broom_0.7.10                                       
## [151] BiocVersion_3.12.0                                 
## [152] later_1.3.0                                        
## [153] httr_1.4.2                                         
## [154] biovizBase_1.38.0                                  
## [155] colorspace_2.0-2                                   
## [156] XML_3.99-0.6                                       
## [157] splines_4.0.3                                      
## [158] statmod_1.4.36                                     
## [159] graphlayouts_0.7.1                                 
## [160] multtest_2.46.0                                    
## [161] systemfonts_1.0.2                                  
## [162] plotly_4.10.0                                      
## [163] xtable_1.8-4                                       
## [164] jsonlite_1.7.2                                     
## [165] tidygraph_1.2.0                                    
## [166] ggfun_0.0.4                                        
## [167] R6_2.5.1                                           
## [168] Hmisc_4.5-0                                        
## [169] pillar_1.6.4                                       
## [170] htmltools_0.5.2                                    
## [171] mime_0.12                                          
## [172] DT_0.19                                            
## [173] glue_1.5.0                                         
## [174] fastmap_1.1.0                                      
## [175] BiocParallel_1.24.1                                
## [176] interactiveDisplayBase_1.28.0                      
## [177] beanplot_1.2                                       
## [178] codetools_0.2-18                                   
## [179] fgsea_1.16.0                                       
## [180] utf8_1.2.2                                         
## [181] bslib_0.3.0                                        
## [182] tibble_3.1.5                                       
## [183] curl_4.3.2                                         
## [184] gtools_3.9.2                                       
## [185] zip_2.2.0                                          
## [186] GO.db_3.12.1                                       
## [187] openxlsx_4.2.4                                     
## [188] openssl_1.4.5                                      
## [189] survival_3.2-13                                    
## [190] rmarkdown_2.11                                     
## [191] munsell_0.5.0                                      
## [192] DO.db_2.9                                          
## [193] rhdf5_2.34.0                                       
## [194] GenomeInfoDbData_1.2.4                             
## [195] HDF5Array_1.18.1                                   
## [196] reshape2_1.4.4                                     
## [197] haven_2.4.3                                        
## [198] gtable_0.3.0